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from __future__ import division, print_function
import numpy as np
from menpo.image import Image
from menpo.fitmultilevel.builder import DeformableModelBuilder
from menpo.fitmultilevel.functions import build_sampling_grid
from menpo.fitmultilevel.featurefunctions import compute_features, sparse_hog
from .classifierfunctions import classifier, linear_svm_lr
class CLMBuilder(DeformableModelBuilder):
r"""
Class that builds Multilevel Constrained Local Models.
Parameters
----------
classifier_type: classifier_closure
A closure implementing a binary classifier.
Examples of such closures can be found in
`menpo.fitmultilevel.clm.classifierfunctions`
patch_shape: tuple of ints
The shape of the patches used by the previous classifier closure.
feature_type: string or function/closure, Optional
If None, the appearance model will be build using the original image
representation, i.e. no features will be extracted from the original
images.
If string or closure, the appearance model will be built from a
feature representation of the original images:
If string, image features will be computed by executing:
feature_image = eval('img.feature_type.' + feature_type + '()')
For this to work properly `feature_type` needs to be one of
menpo's standard image feature methods. Note that, in this case,
the feature computation will be carried out using the default
options.
Non-default feature options and new experimental features can be
defined using functions/closures. In this case, the function must
receive an image as input and return a particular feature
representation of that image. For example:
def igo_double_from_std_normalized_intensities(image)
image = deepcopy(image)
image.normalize_std_inplace()
return image.feature_type.igo(double_angles=True)
See `menpo.image.feature.py` for details more details on
menpo's standard image features and feature options.
Default: None
diagonal_range: int, Optional
All images will be rescaled to ensure that the scale of their
landmarks matches the scale of the mean shape.
If int, ensures that the mean shape is scaled so that
the diagonal of the bounding box containing it matches the
diagonal_range value.
If None, the mean landmarks are not rescaled.
Note that, because the reference frame is computed from the mean
landmarks, this kwarg also specifies the diagonal length of the
reference frame (provided that features computation does not change
the image size).
Default: None
n_levels: int, Optional
The number of multi-resolution pyramidal levels to be used.
Default: 3
downscale: float > 1, Optional
The downscale factor that will be used to create the different
pyramidal levels.
Default: 2
scaled_levels: boolean, Optional
If True, the original images will be both smoothed and scaled using
a Gaussian pyramid to create the different pyramidal levels.
If False, they will only be smoothed.
Default: True
max_shape_components: 0 < int < n_components, Optional
If int, it specifies the specific number of components of the
original shape model to be retained.
Default: None
boundary: int, Optional
The number of pixels to be left as a safe margin on the boundaries
of the reference frame (has potential effects on the gradient
computation).
Default: 3
interpolator:'scipy', Optional
The interpolator that should be used to perform the warps.
Default: 'scipy'
Returns
-------
clm : :class:`menpo.fitmultiple.clm.builder.CLMBuilder`
The CLM Builder object
"""
def __init__(self, classifier_type=linear_svm_lr, patch_shape=(5, 5),
feature_type=sparse_hog, diagonal_range=None, n_levels=3,
downscale=1.1, scaled_levels=True, max_shape_components=None,
boundary=3, interpolator='scipy'):
self.classifier_type = classifier_type
self.patch_shape = patch_shape
self.feature_type = feature_type
self.diagonal_range = diagonal_range
self.n_levels = n_levels
self.downscale = downscale
self.scaled_levels = scaled_levels
self.max_shape_components = max_shape_components
self.boundary = boundary
self.interpolator = interpolator
def build(self, images, group=None, label='all'):
r"""
Builds a Multilevel Constrained Local Model from a list of
landmarked images.
Parameters
----------
images: list of :class:`menpo.image.Image`
The set of landmarked images from which to build the AAM.
group : string, Optional
The key of the landmark set that should be used. If None,
and if there is only one set of landmarks, this set will be used.
Default: None
label: string, Optional
The label of of the landmark manager that you wish to use. If no
label is passed, the convex hull of all landmarks is used.
Default: 'all'
Returns
-------
aam : :class:`menpo.fitmultiple.clm.builder.CLM`
The CLM object
"""
print('- Preprocessing')
self.reference_shape, generator = self._preprocessing(
images, group, label, self.diagonal_range, self.interpolator,
self.scaled_levels, self.n_levels, self.downscale)
print('- Building model pyramids')
shape_models = []
classifiers = []
# for each level
for j in np.arange(self.n_levels):
print(' - Level {}'.format(j))
print(' - Computing feature space')
images = [compute_features(g.next(), self.feature_type)
for g in generator]
# extract potentially rescaled shapes
shapes = [i.landmarks[group][label].lms for i in images]
if j == 0 or self.scaled_levels:
print(' - Building shape model')
shape_model = self._build_shape_model(
shapes, self.max_shape_components)
# add shape model to the list
shape_models.append(shape_model)
print(' - Building classifiers')
sampling_grid = build_sampling_grid(self.patch_shape)
n_points = shapes[0].n_points
level_classifiers = []
for k in range(n_points):
print(' - {} % '.format(round(100*(k+1)/n_points)), end='\r')
positive_labels = []
negative_labels = []
positive_samples = []
negative_samples = []
for i, s in zip(images, shapes):
max_x = i.shape[0] - 1
max_y = i.shape[1] - 1
point = (np.round(s.points[k, :])).astype(int)
patch_grid = sampling_grid + point[None, None, ...]
positive, negative = get_pos_neg_grid_positions(
patch_grid, positive_grid_size=(1, 1))
x = positive[:, 0]
y = positive[:, 1]
x[x > max_x] = max_x
y[y > max_y] = max_y
x[x < 0] = 0
y[y < 0] = 0
positive_sample = i.pixels[positive[:, 0],
positive[:, 1], :]
positive_samples.append(positive_sample)
positive_labels.append(np.ones(positive_sample.shape[0]))
x = negative[:, 0]
y = negative[:, 1]
x[x > max_x] = max_x
y[y > max_y] = max_y
x[x < 0] = 0
y[y < 0] = 0
negative_sample = i.pixels[x, y, :]
negative_samples.append(negative_sample)
negative_labels.append(-np.ones(negative_sample.shape[0]))
positive_samples = np.asanyarray(positive_samples)
positive_samples = np.reshape(positive_samples,
(-1, positive_samples.shape[-1]))
positive_labels = np.asanyarray(positive_labels).flatten()
negative_samples = np.asanyarray(negative_samples)
negative_samples = np.reshape(negative_samples,
(-1, negative_samples.shape[-1]))
negative_labels = np.asanyarray(negative_labels).flatten()
X = np.vstack((positive_samples, negative_samples))
t = np.hstack((positive_labels, negative_labels))
clf = classifier(X, t, self.classifier_type)
level_classifiers.append(clf)
# add level classifiers to the list
classifiers.append(level_classifiers)
# reverse the list of shape and appearance models so that they are
# ordered from lower to higher resolution
shape_models.reverse()
classifiers.reverse()
return CLM(shape_models, classifiers, self.patch_shape,
self.feature_type, self.reference_shape, self.downscale,
self.scaled_levels, self.interpolator)
class CLM(object):
r"""
Constrained Local Model class.
Parameters
-----------
shape_models: :class:`menpo.model.PCA` list
A list containing the shape models of the CLM.
classifiers: classifier_closure list of lists
A list containing the list of classifier_closures per each pyramidal
level of the CLM.
patch_shape: tuple of ints
The shape of the patches used to train the classifiers.
transform: :class:`menpo.transform.PureAlignmentTransform`
The transform used to warp the images from which the AAM was
constructed.
feature_type: str or function
The image feature that was be used to build the appearance_models. Will
subsequently be used by fitter objects using this class to fitter to
novel images.
If None, the appearance model was built immediately from the image
representation, i.e. intensity.
If string, the appearance model was built using one of Menpo's default
built-in feature representations - those
accessible at image.features.some_feature(). Note that this case can
only be used with default feature weights - for custom feature
weights, use the functional form of this argument instead.
If function, the user can directly provide the feature that was
calculated on the images. This class will simply invoke this
function, passing in as the sole argument the image to be fitted,
and expect as a return type an Image representing the feature
calculation ready for further fitting. See the examples for
details.
reference_shape: PointCloud
The reference shape that was used to resize all training images to a
consistent object size.
downscale: float
The constant downscale factor used to create the different levels of
the AAM. For example, a factor of 2 would imply that the second level
of the AAM pyramid is half the width and half the height of the first.
The third would be 1/2 * 1/2 = 1/4 the width and 1/4 the height of
the original.
scaled_levels: boolean
Boolean value specifying whether the AAM levels are scaled or not.
interpolator: string
The interpolator that was used to build the AAM.
Default: 'scipy'
"""
def __init__(self, shape_models, classifiers, patch_shape, feature_type,
reference_shape, downscale, scaled_levels, interpolator):
self.shape_models = shape_models
self.classifiers = classifiers
self.patch_shape = patch_shape
self.feature_type = feature_type
self.reference_shape = reference_shape
self.downscale = downscale
self.scaled_levels = scaled_levels
self.interpolator = interpolator
@property
def n_levels(self):
"""
The number of multi-resolution pyramidal levels of the CLM.
:type: int
"""
return len(self.shape_models)
@property
def n_classifiers_per_level(self):
"""
The number of classifiers per pyramidal level of the CLM.
:type: int
"""
return [len(clf) for clf in self.classifiers]
def instance(self, shape_weights=None, level=-1):
r"""
Generates a novel CLM instance given a set of shape weights. If no
weights are provided, the mean CLM instance is returned.
Parameters
-----------
shape_weights: (n_weights,) ndarray or float list
Weights of the shape model that will be used to create
a novel shape instance. If None, the mean shape
(shape_weights = [0, 0, ..., 0]) is used.
Default: None
level: int, optional
The pyramidal level to be used.
Default: -1
Returns
-------
image: :class:`menpo.shape.PointCloud`
The novel CLM instance.
"""
sm = self.shape_models[level]
# TODO: this bit of logic should to be transferred down to PCAModel
if shape_weights is None:
shape_weights = [0]
n_shape_weights = len(shape_weights)
shape_weights *= sm.eigenvalues[:n_shape_weights] ** 0.5
shape_instance = sm.instance(shape_weights)
return shape_instance
def random_instance(self, level=-1):
r"""
Generates a novel random CLM instance.
Parameters
-----------
level: int, optional
The pyramidal level to be used.
Default: -1
Returns
-------
image: :class:`menpo.shape.PointCloud`
The novel CLM instance.
"""
sm = self.shape_models[level]
# TODO: this bit of logic should to be transferred down to PCAModel
shape_weights = (np.random.randn(sm.n_active_components) *
sm.eigenvalues[:sm.n_active_components]**0.5)
shape_instance = sm.instance(shape_weights)
return shape_instance
def response_image(self, image, group=None, label='all', level=-1):
r"""
Generates a response image result of applying the classifiers of a
particular pyramidal level of the CLM to an image.
Parameters
-----------
image: :class:`menpo.image.base.Image`
The image.
group : string, Optional
The key of the landmark set that should be used. If None,
and if there is only one set of landmarks, this set will be used.
Default: None
label: string, Optional
The label of of the landmark manager that you wish to use. If no
label is passed, the convex hull of all landmarks is used.
Default: 'all'
level: int, optional
The pyramidal level to be used.
Default: -1
Returns
-------
image: :class:`menpo.image.base.Image`
The response image.
"""
image = image.rescale_to_reference_shape(self.reference_shape,
group=group, label=label)
pyramid = image.gaussian_pyramid(n_levels=self.n_levels,
downscale=self.downscale)
images = [compute_features(i, self.feature_type)
for i in pyramid]
images.reverse()
image = images[level]
image_pixels = np.reshape(image.pixels, (-1, image.n_channels))
response_data = np.zeros((image.shape[0], image.shape[1],
self.n_classifiers_per_level[level]))
# Compute responses
for j, clf in enumerate(self.classifiers[level]):
response_data[:, :, j] = np.reshape(clf(image_pixels),
image.shape)
return Image(image_data=response_data)
def get_pos_neg_grid_positions(sampling_grid, positive_grid_size=(1, 1)):
r"""
Divides a sampling grid in positive and negative pixel positions. By
default only the center of the grid is considered to be positive.
"""
positive_grid_size = np.array(positive_grid_size)
mask = np.zeros(sampling_grid.shape[:-1], dtype=np.bool)
center = np.round(np.array(mask.shape) / 2).astype(int)
positive_grid_size -= [1, 1]
start = center - positive_grid_size
end = center + positive_grid_size + 1
mask[start[0]:end[0], start[1]:end[1]] = True
positive = sampling_grid[mask]
negative = sampling_grid[~mask]
return positive, negative
|
jabooth/menpo-archive
|
menpo/fitmultilevel/clm/builder.py
|
Python
|
bsd-3-clause
| 17,337
|
[
"Gaussian"
] |
8e6eeccc5ecb9ff051449f1260aa12abefb9d1b10a75f59f605b80e8e7779335
|
"""Loads configurations from .yaml files and expands environment variables.
"""
import copy
import collections
import glob
import math
import os
import pprint
import sys
import yaml
import toolz as tz
class CmdNotFound(Exception):
pass
# ## Generalized configuration
def update_w_custom(config, lane_info):
"""Update the configuration for this lane if a custom analysis is specified.
"""
name_remaps = {"variant": ["SNP calling", "variant", "variant2"],
"SNP calling": ["SNP calling", "variant", "variant2"],
"variant2": ["SNP calling", "variant", "variant2"]}
config = copy.deepcopy(config)
base_name = lane_info.get("analysis")
if "algorithm" not in config:
config["algorithm"] = {}
for analysis_type in name_remaps.get(base_name, [base_name]):
custom = config.get("custom_algorithms", {}).get(analysis_type)
if custom:
for key, val in custom.iteritems():
config["algorithm"][key] = val
# apply any algorithm details specified with the lane
for key, val in lane_info.get("algorithm", {}).iteritems():
config["algorithm"][key] = val
# apply any resource details specified with the lane
for prog, pkvs in lane_info.get("resources", {}).iteritems():
if prog not in config["resources"]:
config["resources"][prog] = {}
for key, val in pkvs.iteritems():
config["resources"][prog][key] = val
return config
# ## Retrieval functions
def load_system_config(config_file=None, work_dir=None, allow_missing=False):
"""Load bcbio_system.yaml configuration file, handling standard defaults.
Looks for configuration file in default location within
final base directory from a standard installation. Handles both standard
installs (galaxy/bcbio_system.yaml) and docker installs (config/bcbio_system.yaml).
"""
docker_config = _get_docker_config()
if config_file is None:
config_file = "bcbio_system.yaml"
if not os.path.exists(config_file):
base_dir = get_base_installdir()
test_config = os.path.join(base_dir, "galaxy", config_file)
if os.path.exists(test_config):
config_file = test_config
elif allow_missing:
config_file = None
else:
raise ValueError("Could not find input system configuration file %s, "
"including inside standard directory %s" %
(config_file, os.path.join(base_dir, "galaxy")))
config = load_config(config_file) if config_file else {}
if docker_config:
assert work_dir is not None, "Need working directory to merge docker config"
config_file = os.path.join(work_dir, "%s-merged%s" % os.path.splitext(os.path.basename(config_file)))
config = _merge_system_configs(config, docker_config, config_file)
if "algorithm" not in config:
config["algorithm"] = {}
config["bcbio_system"] = config_file
return config, config_file
def get_base_installdir():
return os.path.normpath(os.path.join(os.path.realpath(sys.executable), os.pardir, os.pardir, os.pardir))
def _merge_system_configs(host_config, container_config, out_file=None):
"""Create a merged system configuration from external and internal specification.
"""
out = copy.deepcopy(container_config)
for k, v in host_config.iteritems():
if k in set(["galaxy_config"]):
out[k] = v
elif k == "resources":
for pname, resources in v.iteritems():
if not isinstance(resources, dict) and pname not in out[k]:
out[k][pname] = resources
else:
for rname, rval in resources.iteritems():
if (rname in set(["cores", "jvm_opts", "memory"])
or pname in set(["gatk", "mutect"])):
if pname not in out[k]:
out[k][pname] = {}
out[k][pname][rname] = rval
# Ensure final file is relocatable by mapping back to reference directory
if "bcbio_system" in out and ("galaxy_config" not in out or not os.path.isabs(out["galaxy_config"])):
out["galaxy_config"] = os.path.normpath(os.path.join(os.path.dirname(out["bcbio_system"]),
os.pardir, "galaxy",
"universe_wsgi.ini"))
if out_file:
with open(out_file, "w") as out_handle:
yaml.safe_dump(out, out_handle, default_flow_style=False, allow_unicode=False)
return out
def _get_docker_config():
base_dir = get_base_installdir()
docker_configfile = os.path.join(base_dir, "config", "bcbio_system.yaml")
if os.path.exists(docker_configfile):
return load_config(docker_configfile)
def merge_resources(args):
"""Merge docker local resources and global resource specification in a set of arguments.
Finds the `data` object within passed arguments and updates the resources
from a local docker configuration if present.
"""
docker_config = _get_docker_config()
if not docker_config:
return args
else:
def _update_resources(config):
config["resources"] = _merge_system_configs(config, docker_config)["resources"]
return config
return _update_config(args, _update_resources)
def load_config(config_file):
"""Load YAML config file, replacing environmental variables.
"""
with open(config_file) as in_handle:
config = yaml.load(in_handle)
config = _expand_paths(config)
# lowercase resource names, the preferred way to specify, for back-compatibility
newr = {}
for k, v in config["resources"].iteritems():
if k.lower() != k:
newr[k.lower()] = v
config["resources"].update(newr)
return config
def _expand_paths(config):
for field, setting in config.items():
if isinstance(config[field], dict):
config[field] = _expand_paths(config[field])
else:
config[field] = expand_path(setting)
return config
def expand_path(path):
""" Combines os.path.expandvars with replacing ~ with $HOME.
"""
try:
return os.path.expandvars(path.replace("~", "$HOME"))
except AttributeError:
return path
def get_resources(name, config):
"""Retrieve resources for a program, pulling from multiple config sources.
"""
return tz.get_in(["resources", name], config,
tz.get_in(["resources", "default"], config, {}))
def get_program(name, config, ptype="cmd", default=None):
"""Retrieve program information from the configuration.
This handles back compatible location specification in input
YAML. The preferred location for program information is in
`resources` but the older `program` tag is also supported.
"""
# support taking in the data dictionary
config = config.get("config", config)
try:
pconfig = config.get("resources", {})[name]
# If have leftover old
except KeyError:
pconfig = {}
old_config = config.get("program", {}).get(name, None)
if old_config:
for key in ["dir", "cmd"]:
if not key in pconfig:
pconfig[key] = old_config
if ptype == "cmd":
return _get_program_cmd(name, pconfig, config, default)
elif ptype == "dir":
return _get_program_dir(name, pconfig)
else:
raise ValueError("Don't understand program type: %s" % ptype)
def _get_check_program_cmd(fn):
def wrap(name, pconfig, config, default):
is_ok = lambda f: os.path.isfile(f) and os.access(f, os.X_OK)
bcbio_system = config.get("bcbio_system", None)
if bcbio_system:
system_bcbio_path = os.path.join(os.path.dirname(bcbio_system),
os.pardir, "anaconda", "bin", name)
if is_ok(system_bcbio_path):
return system_bcbio_path
# support bioconda installed programs
if is_ok(os.path.join(os.path.dirname(sys.executable), name)):
return (os.path.join(os.path.dirname(sys.executable), name))
# find system bioconda installed programs if using private code install
program = expand_path(fn(name, pconfig, config, default))
if is_ok(program):
return program
# search the PATH now
for adir in os.environ['PATH'].split(":"):
if is_ok(os.path.join(adir, program)):
return os.path.join(adir, program)
raise CmdNotFound(" ".join(map(repr, (fn.func_name, name, pconfig, default))))
return wrap
@_get_check_program_cmd
def _get_program_cmd(name, pconfig, config, default):
"""Retrieve commandline of a program.
"""
if pconfig is None:
return name
elif isinstance(pconfig, basestring):
return pconfig
elif "cmd" in pconfig:
return pconfig["cmd"]
elif default is not None:
return default
else:
return name
def _get_program_dir(name, config):
"""Retrieve directory for a program (local installs/java jars).
"""
if config is None:
raise ValueError("Could not find directory in config for %s" % name)
elif isinstance(config, basestring):
return config
elif "dir" in config:
return expand_path(config["dir"])
else:
raise ValueError("Could not find directory in config for %s" % name)
def get_jar(base_name, dname):
"""Retrieve a jar in the provided directory
"""
jars = glob.glob(os.path.join(expand_path(dname), "%s*.jar" % base_name))
if len(jars) == 1:
return jars[0]
elif len(jars) > 1:
raise ValueError("Found multiple jars for %s in %s. Need single jar: %s" %
(base_name, dname, jars))
else:
raise ValueError("Could not find java jar %s in %s" %
(base_name, dname))
# ## Retrieval and update to configuration from arguments
def is_std_config_arg(x):
return isinstance(x, dict) and "algorithm" in x and "resources" in x and "files" not in x
def is_nested_config_arg(x):
return isinstance(x, dict) and "config" in x and is_std_config_arg(x["config"])
def get_algorithm_config(xs):
"""Flexibly extract algorithm configuration for a sample from any function arguments.
"""
if isinstance(xs, dict):
xs = [xs]
for x in xs:
if is_std_config_arg(x):
return x["algorithm"]
elif is_nested_config_arg(x):
return x["config"]["algorithm"]
elif isinstance(x, (list, tuple)) and is_nested_config_arg(x[0]):
return x[0]["config"]["algorithm"]
raise ValueError("Did not find algorithm configuration in items: {0}"
.format(pprint.pformat(xs)))
def get_dataarg(args):
"""Retrieve the world 'data' argument from a set of input parameters.
"""
for i, arg in enumerate(args):
if is_nested_config_arg(arg):
return i, arg
elif is_std_config_arg(arg):
return i, {"config": arg}
elif isinstance(arg, (list, tuple)) and is_nested_config_arg(arg[0]):
return i, arg[0]
raise ValueError("Did not find configuration or data object in arguments: %s" % args)
def add_cores_to_config(args, cores_per_job, parallel=None):
"""Add information about available cores for a job to configuration.
Ugly hack to update core information in a configuration dictionary.
"""
def _update_cores(config):
config["algorithm"]["num_cores"] = int(cores_per_job)
if parallel:
parallel.pop("view", None)
config["parallel"] = parallel
return config
return _update_config(args, _update_cores)
def _update_config(args, update_fn):
"""Update configuration, nested in argument list, with the provided update function.
"""
new_i = None
for i, arg in enumerate(args):
if (is_std_config_arg(arg) or is_nested_config_arg(arg) or
(isinstance(arg, (list, tuple)) and is_nested_config_arg(arg[0]))):
new_i = i
break
if new_i is None:
raise ValueError("Could not find configuration in args: %s" % str(args))
new_arg = args[new_i]
if is_nested_config_arg(new_arg):
new_arg["config"] = update_fn(copy.deepcopy(new_arg["config"]))
elif is_std_config_arg(new_arg):
new_arg = update_fn(copy.deepcopy(new_arg))
elif isinstance(arg, (list, tuple)) and is_nested_config_arg(new_arg[0]):
new_arg_first = new_arg[0]
new_arg_first["config"] = update_fn(copy.deepcopy(new_arg_first["config"]))
new_arg = [new_arg_first] + new_arg[1:]
else:
raise ValueError("Unexpected configuration dictionary: %s" % new_arg)
args = list(args)[:]
args[new_i] = new_arg
return args
def convert_to_bytes(mem_str):
"""Convert a memory specification, potentially with M or G, into bytes.
"""
if str(mem_str)[-1].upper().endswith("G"):
return int(mem_str[:-1]) * 1024 * 1024
elif str(mem_str)[-1].upper().endswith("M"):
return int(mem_str[:-1]) * 1024
else:
return int(mem_str)
def adjust_memory(val, magnitude, direction="increase", out_modifier=""):
"""Adjust memory based on number of cores utilized.
"""
modifier = val[-1:]
amount = int(val[:-1])
if direction == "decrease":
new_amount = amount / float(magnitude)
# dealing with a specifier like 1G, need to scale to Mb
if new_amount < 1:
if modifier.upper().startswith("G"):
new_amount = (amount * 1024) / magnitude
modifier = "M" + modifier[1:]
else:
raise ValueError("Unexpected decrease in memory: %s by %s" % (val, magnitude))
amount = int(new_amount)
elif direction == "increase" and magnitude > 1:
# for increases with multiple cores, leave small percentage of
# memory for system to maintain process running resource and
# avoid OOM killers
adjuster = 0.91
amount = int(math.ceil(amount * (adjuster * magnitude)))
if out_modifier.upper().startswith("G") and modifier.upper().startswith("M"):
modifier = out_modifier
amount = int(math.floor(amount / 1024.0))
if out_modifier.upper().startswith("M") and modifier.upper().startswith("G"):
modifier = out_modifier
modifier = int(amount * 1024)
return "{amount}{modifier}".format(amount=amount, modifier=modifier)
def adjust_opts(in_opts, config):
"""Establish JVM opts, adjusting memory for the context if needed.
This allows using less or more memory for highly parallel or multicore
supporting processes, respectively.
"""
memory_adjust = config["algorithm"].get("memory_adjust", {})
out_opts = []
for opt in in_opts:
if opt.startswith("-Xmx") or (opt.startswith("-Xms") and memory_adjust.get("direction") == "decrease"):
arg = opt[:4]
opt = "{arg}{val}".format(arg=arg,
val=adjust_memory(opt[4:],
memory_adjust.get("magnitude", 1),
memory_adjust.get("direction")))
out_opts.append(opt)
return out_opts
# specific program usage
def use_vqsr(algs):
"""Processing uses GATK's Variant Quality Score Recalibration.
"""
vqsr_callers = set(["gatk", "gatk-haplotype"])
vqsr_sample_thresh = 50
vqsr_supported = collections.defaultdict(int)
coverage_intervals = set([])
for alg in algs:
callers = alg.get("variantcaller", "gatk")
if isinstance(callers, basestring):
callers = [callers]
if not callers: # no variant calling, no VQSR
continue
if "vqsr" in alg.get("tools_off", []): # VQSR turned off
continue
for c in callers:
if c in vqsr_callers:
vqsr_supported[c] += 1
coverage_intervals.add(alg.get("coverage_interval", "exome").lower())
if len(vqsr_supported) > 0:
num_samples = max(vqsr_supported.values())
if "genome" in coverage_intervals or num_samples >= vqsr_sample_thresh:
return True
return False
def use_snpeff(algs):
"""Processing uses snpEff. Avoids memory requirements if not used.
"""
return any(alg.get("effects", "snpeff") == "snpeff" and alg.get("variantcaller") for alg in algs)
def use_bcbio_variation_recall(algs):
"""Processing uses bcbio-variation-recall. Avoids core requirement if not used.
"""
for alg in algs:
jointcaller = alg.get("jointcaller", [])
if not isinstance(jointcaller, (tuple, list)):
jointcaller = [jointcaller]
for caller in jointcaller:
if caller not in set(["gatk-haplotype-joint", None, False]):
return True
return False
## functions for navigating through the standard galaxy directory of files
def get_rRNA_interval(genome_dir):
return os.path.join(genome_dir, "rnaseq", "rRNA.interval_list")
def get_transcript_refflat(genome_dir):
return os.path.join(genome_dir, "rnaseq", "ref-transcripts.refFlat")
def get_rRNA_sequence(genome_dir):
return os.path.join(genome_dir, "rnaseq", "rRNA.fa")
def program_installed(program, data):
"""
returns True if the path to a program can be found
"""
try:
path = get_program(program, data)
except CmdNotFound:
return False
return True
|
mjafin/bcbio-nextgen
|
bcbio/pipeline/config_utils.py
|
Python
|
mit
| 17,799
|
[
"Bioconda",
"Galaxy"
] |
51f54bce9d3bc477302abf2759cb18bfdfde93d8731df2a25bef8965d4ba3742
|
# Custom library
import data_reader
# Standard libraries
import datetime
import os
import sys
import time
# Third-party libraries
import numpy as np
import tensorflow as tf
sess = tf.InteractiveSession()
# Short form of Boolean value
T, F = True, False
# Training/ classification setting ---------------------------------------------------
# This code can be used to train the neural network by setting train_neural_network
# to (T) or it can also be used for performing classification using labelled data
# by setting train_neural_network to (F) and perform_classification_with_label to
# (T) or it can also be used for performing classification using raw unlabelled
# data by setting train_neural_network to (F) and perform_classification_with_label
# to (F).
train_neural_network = T
continue_training_using_trained_model = T
# Number of training epoch
epochs = 100
# Size of training batch
batch_size = 200
# Threshold of difference between train_accuracy and test_accuracy
delta_accuracy_threshold = 0.025
# Threshold for stopping training when overtraining is encountered.
overtraining_threshold = 10
# Classification can be performed on labelled or raw data. Set
# perform_classification_with_label to (F) to perform classification on labelled
# data or (T) to perform classification on raw data. When train_neural_network is
# set to (T), perform_classification_with_label is set to (T) automatically and
# clasification will be done on labelled data.
perform_classification_with_label = T
# System and file information --------------------------------------------------------
# Potential energy
U = 9
# System size
# number of spin in each of the cube dimension
n_x = 4
# number of imaginary time dimension
L = 200
# Volume of tesseract
V4d = L*(n_x)**3
# Critical temperature
Tc = 0.36
# Number of data per file
ndata_per_temp = 1000
# Number of classification data (raw unlabelled data) to be used for classification.
classification_data_per_temp = 250
# String of current date and time
dt = datetime.datetime.now()
year, month, day, hour, minute = '%.2d' % dt.year, '%.2d' % dt.month, '%.2d' % dt.day, '%.2d' % dt.hour, '%.2d' % dt.minute
start_date_time = '%s%s%s-%s%s' % (year, month, day, hour, minute)
# Input labelled and shuffled filename for training and performaing classification
# with labels.
filename = './N%dx%dx%d_L%d_U%d_Mu0_T_shuffled' % (n_x,n_x,n_x,L,U) + '_%.2d.dat'
# Input raw filename for performing classification without labels.
rawdata_filename = './N%dx%dx%d_L%d_U%d_Mu0_T' % (n_x,n_x,n_x,L,U) + '%s.HSF.stream'
# Trained model
filename_trained_model = "./model.ckpt"
# Output model filename
filename_weight_bias = "./model_" + start_date_time + ".ckpt"
# Output of training measurements filename
filename_measure = "./measurements_" + start_date_time + ".dat"
# Output of classification result with labels
filename_result = "./result_" + start_date_time + ".dat"
# Output of classification result from raw data (without labels)
filename_classified = "./classified_" + start_date_time + ".dat"
# Neural network architecture settings -----------------------------------------------
# Feature extraction layer(s)
n_feature_map1 = 64
n_feature_map2 = 27
# Classification layer
n_fully_connected_neuron = 27
n_output_neuron = 2
# Spatial filter size: filter depth, height, and width
filter_d = 2
filter_h = filter_d
filter_w = filter_d
# Adaptive learning rate is used. As the training goes on, the learning rate is
# lowered progressively using exponential decay function.
# Optimizer initial learning rate
eta0 = 1e-3
# decay rate
decay_rate = 0.83
# L2 regularization parameter
lambdha_per_n_train_data = 0.0001
# Don't change any of the following variables.
if train_neural_network == T :
print 'Process: training.'
# xxxxx Don't change the following variable. xxxxx
# Perform classification on test data after training.
perform_classification_with_label = T
# xxxxx Don't change the following variable. xxxxx
# When perform_classification is set to True, both training and test data are
# to be loaded.
perform_classification = F
else :
# Set continue_training_if_model_not_found to T to proceed with training when no
# previously trained model is found in the directory or set it to F to input the
# appropriate model filename.
continue_training_if_model_not_found = F
# xxxxx Don't change the following variable. xxxxx
if perform_classification_with_label == T :
print 'Process: classification with label.'
else :
print 'Process: classification without label.'
print 'Using %d data per temperature.' % classification_data_per_temp
# xxxxx Don't change the following variable. xxxxx
# When perform_classification is set to True, only test data will be loaded.
perform_classification = T
if perform_classification_with_label == True :
# Get temperature and save them to a file.
os.system("ls -l N%dx%dx%d_L%d_U%d_Mu0_T*.HSF.stream | awk '{print $9}' | sed -e s/N%dx%dx%d_L%d_U%d_Mu0_T//g -e s/.HSF.stream//g > dtau.dat" %(n_x,n_x,n_x,L,U,n_x,n_x,n_x,L,U))
dtau = np.genfromtxt("dtau.dat")
# Array of shuffled file's file number
filenumber = np.arange(1,len(dtau)+1,1)
# Provide file information to the data_reader module.
HSF = data_reader.insert_file_info(filename,filenumber, performing_classification=perform_classification)
# Load and catogorize data into either training data, test data, validation data, or
# all of them. If validation data is needed, set include_validation_data to (T)
# in the insert_file_info() module above.
HSF = HSF.categorize_data()
else :
# Get temperature and save them to a file.
os.system("ls -l N%dx%dx%d_L%d_U%d_Mu0_T*.HSF.stream | awk '{print $9}' | sed -e s/N%dx%dx%d_L%d_U%d_Mu0_T//g -e s/.HSF.stream//g > dtau.dat" %(n_x,n_x,n_x,L,U,n_x,n_x,n_x,L,U))
# Load temperature into a list of string
dtau = np.genfromtxt("dtau.dat",dtype='str')
# The number of lines to skip at the beginning of the file if not all of the data is
# to be loaded.
sh = ndata_per_temp - classification_data_per_temp
while ( ndata_per_temp - sh - classification_data_per_temp ) < 0 :
print 'Sum of classification data per temperature and the number of lines skip at the beginning of the file must be equal to number of data per temnperature.'
print 'Number of data per temnperature : %d' % ndata_per_temp
print 'Classification data used per temperature : %d' % classification_data_per_temp
print 'Number of lines skip at the beginning of the file: %d' % sh
classification_data_per_temp = input('Input new classification data used per temperature: ')
sh = input('Input number of lines skip at the beginning of the file: ')
# Provide file information to the data_reader module.
HSF = data_reader.insert_file_info(rawdata_filename,dtau)
# Load classification data.
HSF = HSF.load_classification_data(nrows=ndata_per_temp, ncols=n_x*n_x*n_x*L,
SkipHeader=sh, load_ndata_per_file=classification_data_per_temp)
if train_neural_network == T or not(perform_classification) :
n_train_data = len(HSF.train.labels)
while np.modf(float(n_train_data)/batch_size)[0] > 0.0 :
print 'Warning! Number of data/ batch size must be an integer.'
print 'Number of data: %d' % n_train_data
print 'Batch size : %d' % batch_size
batch_size = int(input('Input new batch size: '))
# Number of training cycle per training epoch
iteration_per_epoch=n_train_data/batch_size
print 'Number of training data: %d' % n_train_data
elif train_neural_network == F and perform_classification_with_label :
n_train_data = len(dtau)*ndata_per_temp - len(HSF.test.labels)
print 'Number of training data: %d' % n_train_data
else :
n_train_data = -1
while n_train_data < 0 :
n_train_data = input('Number of training data used:' )
# x is a 2D-tensor and None means that a dimesion can be of any length,
# but in this case, it corresponds to the batch size. To start building
# the computation graph, we'll create nodes for input images and target
# output classes. The target output classes y_ will consist of a 2D
# tensor, where each row is a one-hot (one-hot refers to a groups of
# bits among which only one is (1), the opposite is called one-cold) 2
# -dimensional vector vector indicating which digit class the
# corresponding HSF data belongs to.
x = tf.placeholder(tf.float32, [None, n_x*n_x*n_x * L])
y_ = tf.placeholder(tf.float32, [None, n_output_neuron])
# To prevent 0 gradients and break symmetry, one should genereally
# initialize weights with a small amount of noise for symmetry breaking.
# To avoid "dead neurons" when using ReLU neurons, it is also a good
# practice to initalize them with a slightly positive initial bias.
def weight_variable(shape):
initial = tf.truncated_normal(shape, stddev=0.1)
return tf.Variable(initial)
def bias_variable(shape):
initial = tf.constant(0.1, shape=shape)
return tf.Variable(initial)
def conv3d(x, W, pad='VALID'):
# The convolutions uses a stride of one and are zero padded so that
# the output is the same size as the input.
# tf.nn.conv3d(input, filter, strides, padding, name=None)
return tf.nn.conv3d(x, W, strides = [1,1,1,1,1], padding=pad)
def max_pool_2x2x2(x, pad='SAME'):
# Max pooling over 2x2 blocks.
# tf.nn.max_pool(input, ksize, strides, padding,
# data_format='NHWC', name=None)
# input : shape [batch, depth, rows, cols, channels]
# ksize : The size of the max pool window for each dimension of the
# input tensor
# strides : The stride of the sliding window for each dimension of
# the input tnesor.
return tf.nn.max_pool3d(x, ksize=[1,2,2,2,1],
strides=[1,2,2,2,1], padding=pad)
# Feature extraction layer -----------------------------------------------------------
# First Convolution Layer
# The convolution will compute n features for each mxmxm block. Its weight
# tensor will have a shape of [filter_Depth, filter_height, filter_width,
# in_channels, out_channels].
W_conv1 = weight_variable([filter_d,filter_h,filter_w,L,n_feature_map1])
b_conv1 = bias_variable([n_feature_map1])
# To apply the layer, first reshape x to a 4D tensor, with the second and
# third dimensions correspondings to image width and height, and the final
# dimension corresponding to the number of color channels.
x_image = tf.reshape(x, [-1,n_x,n_x,n_x,L])
# Then convolve x_image with the weight tensor, add the bias, apply the
# ReLU function. Since no padding is used in conv3d, i.e. padding = 'VALID',
# the output size : n_feature_map1 x n_x-1 x n_x-1 x n_x-1
h_conv1 = tf.nn.relu(conv3d(x_image, W_conv1) + b_conv1)
# Second Convolution Layer
W_conv2 = weight_variable([filter_d,filter_h,filter_w,n_feature_map1,n_feature_map2])
b_conv2 = bias_variable([n_feature_map2])
h_conv2 = tf.nn.relu(conv3d(h_conv1, W_conv2) + b_conv2)
# Classification layer ---------------------------------------------------------------
# Fully-connected Layer
# Now add a fully-connected layer with n_fully_connected_neuron neurons to
# allow processing on the entire image. The tensor from the previous layer
# is reshaped into a batch of vectors, multiply by a weight matrix, add a
# bias, and apply a ReLU.
W_fc1 = weight_variable([n_feature_map2*(n_x-2)**3, n_fully_connected_neuron])
b_fc1 = bias_variable([n_fully_connected_neuron])
h_conv2_flat = tf.reshape(h_conv2, [-1, n_feature_map2*(n_x-2)**3])
h_fc1 = tf.nn.relu(tf.matmul(h_conv2_flat, W_fc1) + b_fc1)
# Dropout
# To reduce overfitting, dropout will be applied before the readout layer.
# We'll create a placeholder for the probability that a neuron's output is
# kept during dropout. This allows us tro turn dropout on during training, and
# turn it off during testing. TensorFlow's tf.nn.dropout op automatically
# handles scaling neuron outputs in addition to masking them, so droput just
# works without any additional scaling.
keep_prob = tf.placeholder(tf.float32)
h_fc1_drop = tf.nn.dropout(h_fc1, keep_prob)
# Readout layer
# Finally, a softmax regression layer is added.
W_fc2 = weight_variable([n_fully_connected_neuron,n_output_neuron])
b_fc2 = bias_variable([n_output_neuron])
y_conv = tf.nn.softmax(tf.matmul(h_fc1_drop, W_fc2) + b_fc2)
# Train and Evaluate the Model
L2_reg = lambdha_per_n_train_data*(tf.nn.l2_loss(W_fc1) + tf.nn.l2_loss(W_fc2))
cross_entropy = tf.reduce_mean(-tf.reduce_sum(y_ * tf.log(y_conv)+L2_reg, reduction_indices=[1]))
# tf.train.exponential_decay(learning_rate, global_step, decay_steps, decay_rate, staircase=False)
# Use adaptive learning rate
global_step = tf.Variable(0, trainable=False)
eta = tf.train.exponential_decay(eta0, global_step*batch_size, n_train_data, decay_rate)
train_step = tf.train.AdamOptimizer(eta).minimize(cross_entropy, global_step=global_step)
correct_prediction = tf.equal(tf.argmax(y_conv,1), tf.argmax(y_,1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
# Before Variables can be used within a session, they must be initialized
# using that session.
sess.run(tf.initialize_all_variables())
# When performing classification, check if the trained model checkpoint file is
# located in the current file directory before restoring.
if train_neural_network == False :
if os.path.isfile(filename_trained_model) == False and continue_training_if_model_not_found :
print '%s is not found in the current directory, starting training...' % filename_trained_model
train_neural_network = True
continue_training_using_trained_model = False
else :
while not(os.path.isfile(filename_trained_model)) :
print '%s is not found in the current directory.' % filename_trained_model
filename_trained_model = raw_input('Input trained model filename: ')
filename_trained_model = './' + filename_trained_model
train_neural_network = False
# Training ---------------------------------------------------------------------------
# Training the model can be accomplished by repeatedly running train_step. Each
# training iteration load n training examples. Then, the train_step operation can be
# run using feed_dict to replace the placeholder tensors x and y_ with the training
# examples. Note: any tensor in the computation graph can be replcaed using feed_dict.
start_time = time.time()
if train_neural_network :
# Check if the trained model checkpoint file is located in the current file directory
# before restoring.
if continue_training_using_trained_model :
skip = False
file_exist = os.path.isfile(filename_trained_model)
while (not(file_exist) and not(skip)) :
print '%s is not found in the current directory.' % filename_trained_model.replace('./','')
skip = raw_input('Select T to start training from scratch or F to enter the filename of another trained model: ')
while skip not in ['T','F']:
skip = raw_input('Select T or F: ')
if skip == 'T' :
skip = True
else :
skip = False
if skip :
file_exist = False
else :
filename_trained_model = raw_input('Input trained model filename: ')
while not(os.path.isfile(filename_trained_model)) :
print '%s is not found in the current directory.'% filename_trained_model.replace('./','')
filename_trained_model = raw_input('Input trained model filename: ')
filename_trained_model = './' + filename_trained_model
if os.path.isfile(filename_trained_model) :
skip = True
if file_exist :
print 'Continue training using %s.' % filename_trained_model.replace('./','')
saver = tf.train.Saver([W_conv1, b_conv1, W_conv2, b_conv2, W_fc1, b_fc1, W_fc2, b_fc2])
# Restore trained model.
save_path = saver.restore(sess, filename_trained_model)
# Initialize best test accuracy.
best_test_accuracy = 0.85
# Calculate the number of data to collect for the whole training cycle.
ndata_collect_per_epoch = round(float(n_train_data)/batch_size/100)
if ndata_collect_per_epoch > 1 :
ndata_collect = int(ndata_collect_per_epoch*epochs)
else :
ndata_collect = int(epochs)
# Initialise data table.
# First column : Training epochs
# Second column: Training accuracy
# Third column : Testing accuracy
# Fourth column: Cost
Table_measure = np.zeros(( ndata_collect, 4))
# Initialise the counter for number of data collected.
n = 0
fractional_epoch = batch_size*100/float(n_train_data)
print 'Total number of training epochs: %.1f' % (ndata_collect*fractional_epoch)
# Initialise counter for checking overtraining/ overfitting.
n_overtraining_counter = 0
m = 0
Overtraining = False
for j in range(epochs):
# Break out of the training epoch loop if overtraining is encountered.
if Overtraining :
break
for i in range(iteration_per_epoch):
batch = HSF.train.next_batch(batch_size)
if i%100 == 0:
train_accuracy = accuracy.eval(feed_dict={
x: batch[0], y_: batch[1], keep_prob: 1.0})
test_accuracy = accuracy.eval(feed_dict={
x: HSF.test.images, y_: HSF.test.labels, keep_prob: 1.0})
Cost = cross_entropy.eval(feed_dict={x: batch[0], y_: batch[1], keep_prob: 1.0})
print '%.2fs, epoch %.2f, training accuracy %g, test accuracy %g, cost %g' % (time.time()-start_time,(n+1)*fractional_epoch, train_accuracy, test_accuracy, Cost)
Table_measure[n,0] = n*fractional_epoch
Table_measure[n,1] = train_accuracy
Table_measure[n,2] = test_accuracy
Table_measure[n,3] = Cost
# To avoid multiple training, the model is saved when the difference between testing
# accuracy and training accuracy doesn't exceed a set value (it is set to 0.05 here)
# and if the current testing accuracy is higher than the previous.
delta_accuracy = train_accuracy - test_accuracy
if (test_accuracy > best_test_accuracy) and (delta_accuracy <= delta_accuracy_threshold) and (delta_accuracy > 0) :
# Update the best test accuracy
best_test_accuracy = test_accuracy
# Save the best model thus far if the above two criteria are met.
print 'Saving model %s and measurements %s.' % (filename_weight_bias.replace('./',''), filename_measure.replace('./',''))
saver = tf.train.Saver([W_conv1, b_conv1, W_conv2, b_conv2, W_fc1, b_fc1, W_fc2, b_fc2])
save_path = saver.save(sess, filename_weight_bias)
check_model = tf.reduce_mean(W_conv1).eval()
best_epoch = n*fractional_epoch
np.savetxt(filename_measure, Table_measure[:n+1,:])
# Check for overtraining/ overfitting. If so, stop training and break out of the
# training iteration per epoch loop.
if train_accuracy > test_accuracy and test_accuracy > 0.8 :
if m == 0 :
# If training accuracy is greater than test accuracy on first account, set
# counter to 1.
n_overtraining_counter = 1
m = n
elif (m+1) == n :
# If training accuracy is greater than test accuracy consecutively, increase
# counter.
n_overtraining_counter += 1
m = n
elif (m+1) < n :
# Reset counter otherwise.
n_overtraining_counter = 0
m = 0
if n_overtraining_counter >= overtraining_threshold or np.isnan(Cost):
print 'Overtraining encountered. Stopping training.'
Table_measure = Table_measure[:n+1,:]
Overtraining = True
break
else :
Overtraining = False
n += 1
train_step.run(feed_dict={x: batch[0], y_: batch[1], keep_prob: 0.5})
if not(Overtraining) :
# Final check to save the best model.
train_accuracy = accuracy.eval(feed_dict={
x: batch[0], y_: batch[1], keep_prob: 1.0})
test_accuracy = accuracy.eval(feed_dict={
x: HSF.test.images, y_: HSF.test.labels, keep_prob: 1.0})
Cost = cross_entropy.eval(feed_dict={x: batch[0], y_: batch[1], keep_prob: 1.0})
delta_accuracy = abs(train_accuracy - test_accuracy)
if test_accuracy > best_test_accuracy :
if (delta_accuracy <= delta_accuracy_threshold) and delta_accuracy > 0 :
print 'Saving model...'
saver = tf.train.Saver([W_conv1, b_conv1, W_conv2, b_conv2, W_fc1, b_fc1, W_fc2, b_fc2])
save_path = saver.save(sess, filename_weight_bias)
check_model = tf.reduce_mean(W_conv1).eval()
best_epoch = ndata_collect*fractional_epoch
print '%.2fs, epoch %.2f, training accuracy %g, test accuracy %g, cost %g' % (time.time()-start_time,(n+1)*fractional_epoch, train_accuracy, test_accuracy, Cost)
print 'Best training epoch: %g' % best_epoch
print 'Model saved in file: ', save_path
# To proceed, load the best (saved) model instead of the last training model.
saver.restore(sess, filename_weight_bias)
# Check if the saved model and the restored model are the same.
if check_model != tf.reduce_mean(W_conv1).eval() :
print 'Warning! Best training model and the restored model is incompatible. Exiting...'
sys.exit()
# Save the measurements:
# First column : Training epochs
# Second column: Training accuracy
# Third column : Testing accuracy
# Fourth column: Cost
np.savetxt(filename_measure, Table_measure)
# Classification ---------------------------------------------------------------------
else :
saver = tf.train.Saver([W_conv1, b_conv1, W_conv2, b_conv2, W_fc1, b_fc1, W_fc2, b_fc2])
# To proceed, load the trained model.
saver.restore(sess, filename_trained_model)
print 'Performing classification using %s.' % filename_trained_model.replace('./','')
# Classification with labels ---------------------------------------------------------
if perform_classification_with_label == True :
# First column : Temperature
# Second column: Average classified output of the second neuron
# Third column : Average classified output of the first neuron
# Fourth column: Classification accuracy
# Fifth column : Number of data used
Table = np.zeros(( len(dtau), 5))
Table[:,0] = dtau
for i in range(len(HSF.test.temps)) :
# Output of neural net vs temperature
Table[HSF.test.temps[i],1] += np.argmax(y_conv.eval(feed_dict={x: HSF.test.images[i,:].reshape(1,V4d), keep_prob: 1.0}))
# Accuracy vs temperature
Table[HSF.test.temps[i],3] += accuracy.eval(feed_dict={x: HSF.test.images[i,:].reshape(1,V4d), y_: HSF.test.labels[i,:].reshape(1,n_output_neuron), keep_prob: 1.0})
Table[HSF.test.temps[i],-1] += 1
# Normalize the output of the second neuron
Table[:,1] = Table[:,1]/Table[:,-1].astype('float')
# Normalized output of the first neuron
Table[:,2] = 1.0-Table[:,1]
# Normalize the classification accuracy
Table[:,3] = Table[:,3]/Table[:,-1].astype('float')
np.savetxt(filename_result, Table)
print 'Result saved as %s.' % filename_result
# Classification on raw data --------------------------------------------------------
else :
# First column : Temperature
# Second column: Average classified output of the second neuron
# Third column : Average classified output of the first neuron
# Fourth column: Number of data used
Table = np.zeros(( len(dtau), 4))
Table[:,0] = dtau
Table[:,-1] = classification_data_per_temp
n=0
for j in range(len(dtau)) :
for i in range(classification_data_per_temp) :
# Output of neural net vs temperature
Table[j,1] += np.argmax(y_conv.eval(feed_dict={x: HSF.classification.images[n,:].reshape(1,V4d), keep_prob: 1.0}))
n+=1
# Normalize the output of the second neuron
Table[:,1] = Table[:,1]/Table[:,-1].astype('float')
# Normalized output of the first neuron
Table[:,2] = 1.0-Table[:,1]
np.savetxt(filename_classified, Table)
print 'Classified result saved as %s.' % filename_classified
|
kchng/Quantum_machine_learning
|
TF_HSF_CNN1.py
|
Python
|
apache-2.0
| 24,088
|
[
"NEURON"
] |
fe9438f31938e1f220593cb04087c91b7991e0b347ac0f04ed9476cf9d9b4601
|
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for writer cjsonwriter module."""
import os
import unittest
import json
import cclib
__filedir__ = os.path.dirname(__file__)
__filepath__ = os.path.realpath(__filedir__)
__datadir__ = os.path.join(__filepath__, "..", "..")
class CJSONTest(unittest.TestCase):
def setUp(self):
self.CJSON = cclib.io.CJSONWriter
def test_init(self):
"""Does the class initialize correctly?"""
fpath = os.path.join(__datadir__, "data/ADF/basicADF2007.01/dvb_gopt.adfout")
data = cclib.io.ccopen(fpath).parse()
cjson = cclib.io.cjsonwriter.CJSON(data)
# The object should keep the ccData instance passed to its constructor.
self.assertEqual(cjson.ccdata, data)
def test_cjson_generation(self):
"""Does the CJSON format get generated properly?"""
fpath = os.path.join(__datadir__, "data/ADF/basicADF2007.01/dvb_gopt.adfout")
data = cclib.io.ccopen(fpath).parse()
cjson = cclib.io.cjsonwriter.CJSON(data).generate_repr()
# The data available in the cjson and ccdata objects should be equal.
json_data = json.loads(cjson)
number_of_atoms = json_data['properties']['number of atoms']
self.assertEqual(number_of_atoms, data.natom)
if __name__ == "__main__":
unittest.main()
|
Schamnad/cclib
|
test/io/testcjsonwriter.py
|
Python
|
bsd-3-clause
| 1,509
|
[
"ADF",
"cclib"
] |
cdffb3078c9b175839fcd5f47b4f0d5b9e8f667ee5bedd71ee7eefccf080fe85
|
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
from typing import Dict
from kivy import Logger
try:
import netifaces
except Exception as ex:
Logger.error("Can't load netifaces:"+str(ex))
__all__ = ['GetGatewayV6']
def GetGatewayV6() -> str:
uIP:str = u'FE80::1'
uFamily:str = u'AF_INET6'
iInet_num:int
try:
iInet_num = getattr(netifaces, uFamily)
dGateways:Dict = netifaces.gateways()
# noinspection PyTypeChecker
uIP = dGateways['default'][iInet_num][0]
except Exception:
# Logger.error("Error on GetGatewayV6:"+str(e))
pass
return uIP
|
thica/ORCA-Remote
|
src/ORCA/utils/Platform/generic/generic_GetGatewayV6.py
|
Python
|
gpl-3.0
| 1,463
|
[
"ORCA"
] |
0014e4a56e5db8eba86cf6cb4b94bbe63652cbc644d442b0d68ad49bb815b3ba
|
"""
Module for support V_sim ascii fileformat
Contains routines to load .ascii files and
create pychemia Structure objects and to save
back to .ascii files
This code was originally created for ASE
"""
import re as _re
from pychemia.utils.constants import bohr_angstrom
from pychemia.core import Structure
def load(filep):
"""
Read an V_sim .ascii file and returns a pychemia
Structure object
Args:
filep: (string) Path to a .ascii file or an
actual file-like object
Returns:
struct: (object) A pychemia Structure object
"""
if isinstance(filep, str):
f = open(filep)
else: # Assume it's a file-like object
f = filep
comment = f.readline()
line = f.readline() + ' ' + f.readline()
box = line.split()
for i in range(len(box)):
box[i] = float(box[i])
keywords = []
positions = []
symbols = []
re_comment = _re.compile('^\s*[#!]')
re_node = _re.compile('^\s*\S+\s+\S+\s+\S+\s+\S+')
while True:
line = f.readline()
if line == '':
break # EOF -> Exit
p = re_comment.match(line)
if p is not None:
# remove comment character at the beginning of line
line = line[p.end():].replace(',', ' ').lower()
if line[:8] == "keyword:":
keywords.extend(line[8:].split())
elif re_node.match(line):
unit = 1.0
if not ("reduced" in keywords):
if ("bohr" in keywords) or ("bohrd0" in keywords) or ("atomic" in keywords) or ("atomicd0" in keywords):
unit = bohr_angstrom
fields = line.split()
positions.append([unit * float(fields[0]),
unit * float(fields[1]),
unit * float(fields[2])])
symbols.append(fields[3])
f.close()
if ("surface" in keywords) or ("freeBC" in keywords):
raise NotImplementedError
# create atoms object based on the information
if "angdeg" in keywords:
cell = cell.par_to_cell(box)
else:
unit = 1.0
if ("bohr" in keywords) or ("bohrd0" in keywords) or ("atomic" in keywords) or ("atomicd0" in keywords):
unit = bohr_angstrom
cell = [[unit * box[0], 0.0, 0.0],
[unit * box[1], unit * box[2], 0.0],
[unit * box[3], unit * box[4], unit * box[5]]]
if "reduced" in keywords:
struct = Structure(cell=cell, reduced=positions, symbols=symbols, name=comment)
else:
struct = Structure(cell=cell, positions=positions, symbols=symbols, name=comment)
return struct
def save(struct, filep, cartesian=True, long_format=True, angdeg=False):
"""
Saves a pychemia Structure object in V_sim .ascii fileformat
in the simplest way, i.e. using all
defaults with no optional keywords. In the first line we add the
number of atoms, as this is used by certain code
"""
if isinstance(filep, str):
f = open(filep, 'w')
else: # Assume it's a 'file-like object'
f = filep
# write header (treated as a comment by v_sim
f.write("%s\n" % struct.name)
# write cell
cell = struct.cell
if angdeg:
ddd = cell_to_cellpar(cell)
else:
ddd = cell_to_reduced(cell)
f.write("%.14f %.14f %.14f\n" % (ddd[0], ddd[1], ddd[2]))
f.write("%.14f %.14f %.14f\n" % (ddd[3], ddd[4], ddd[5]))
if angdeg:
f.write("#keyword: angdeg\n")
# Write atom positions in scaled or cartesian coordinates
if cartesian:
coord = struct.positions
else:
f.write("#keyword: reduced\n")
coord = struct.reduced
if long_format:
cform = ' %19.16f'
else:
cform = ' %9.6f'
symbols = struct.symbols
for iatom, atom in enumerate(coord):
f.write(' ')
for dcoord in atom:
f.write(cform % dcoord)
f.write(' ' + symbols[iatom] + '\n')
def cell_to_reduced(full):
"""
Transforms the given matrix full into a reduced array used by
V_Sim to store box definition.
translated from src/coreTools/toolMatrix.c
subroutine tool_matrix_reducePrimitiveVectors
"""
from numpy import zeros
from numpy.linalg import norm
xcoord = full[0].copy()
# Compute the Y vector of the new basis, orthogonal to xcoord an coplanar with xcoord and old y vector
u = zeros(3)
u[0] = full[0][1] * full[1][2] - full[0][2] * full[1][1]
u[1] = full[0][2] * full[1][0] - full[0][0] * full[1][2]
u[2] = full[0][0] * full[1][1] - full[0][1] * full[1][0]
deltaij = xcoord[0] * u[1] - xcoord[1] * u[0]
if deltaij != 0.0:
i = 0
j = 1
k = 2
else:
deltaij = xcoord[0] * u[2] - xcoord[2] * u[0]
if deltaij != 0.0:
i = 0
j = 2
k = 1
else:
deltaij = xcoord[1] * u[2] - xcoord[2] * u[1]
if deltaij != 0.0:
i = 1
j = 2
k = 0
else:
# Error
return None
y = zeros(3)
y[k] = -1.0
y[i] = (xcoord[k] * u[j] - xcoord[j] * u[k]) / deltaij
y[j] = (xcoord[i] * u[k] - xcoord[k] * u[i]) / deltaij
# We need to turn Y if y.Y is negative
fnorm = full[1][0] * y[0] + full[1][1] * y[1] + full[1][2] * y[2]
if fnorm < 0.0:
y *= -1.
# Compute the new Z vector in order to form a direct orthogonal
# basis with xcoord and Y
z = zeros(3)
z[0] = xcoord[1] * y[2] - xcoord[2] * y[1]
z[1] = xcoord[2] * y[0] - xcoord[0] * y[2]
z[2] = xcoord[0] * y[1] - xcoord[1] * y[0]
# Normalize vectors
xcoord /= norm(xcoord)
y /= norm(y)
z /= norm(z)
# Compute the reduce value for the basis.
reduced = zeros(6)
reduced[0] = xcoord[0] * full[0][0] + xcoord[1] * full[0][1] + xcoord[2] * full[0][2]
reduced[1] = xcoord[0] * full[1][0] + xcoord[1] * full[1][1] + xcoord[2] * full[1][2]
reduced[2] = y[0] * full[1][0] + y[1] * full[1][1] + y[2] * full[1][2]
reduced[3] = xcoord[0] * full[2][0] + xcoord[1] * full[2][1] + xcoord[2] * full[2][2]
reduced[4] = y[0] * full[2][0] + y[1] * full[2][1] + y[2] * full[2][2]
reduced[5] = z[0] * full[2][0] + z[1] * full[2][1] + z[2] * full[2][2]
return reduced
|
MaterialsDiscovery/PyChemia
|
pychemia/io/ascii.py
|
Python
|
mit
| 6,387
|
[
"ASE"
] |
afa804a022dc296d0a95fdb513039676d1a18563fbe5c40c975d233c6e3772eb
|
import pkg_resources
import sys
if sys.version_info < (3, 6):
raise EnvironmentError('Hail requires Python 3.6 or later, found {}.{}'.format(
sys.version_info.major, sys.version_info.minor))
__pip_version__ = pkg_resources.resource_string(__name__, 'hail_pip_version').decode().strip()
del pkg_resources
del sys
__doc__ = r"""
__ __ <>__
/ /_/ /__ __/ /
/ __ / _ `/ / /
/_/ /_/\_,_/_/_/
===================
For API documentation, visit the website: https://www.hail.is
For help, visit either:
- the forum: https://discuss.hail.is
- or our Zulip chatroom: https://hail.zulipchat.com
To report a bug, please open an issue: https://github.com/hail-is/hail/issues
"""
# F403 'from .expr import *' used; unable to detect undefined names
# F401 '.expr.*' imported but unused
# E402 module level import not at top of file
from .table import Table, GroupedTable, asc, desc # noqa: E402
from .matrixtable import MatrixTable, GroupedMatrixTable # noqa: E402
from .expr import * # noqa: F401,F403,E402
from .genetics import * # noqa: F401,F403,E402
from .methods import * # noqa: F401,F403,E402
from . import expr # noqa: E402
from . import genetics # noqa: E402
from . import methods # noqa: E402
from . import stats # noqa: E402
from . import linalg # noqa: E402
from . import plot # noqa: E402
from . import experimental # noqa: E402
from . import ir # noqa: E402
from . import backend # noqa: E402
from . import nd # noqa: E402
from hail.expr import aggregators as agg # noqa: E402
from hail.utils import (Struct, Interval, hadoop_copy, hadoop_open, hadoop_ls, # noqa: E402
hadoop_stat, hadoop_exists, hadoop_is_file,
hadoop_is_dir, copy_log)
from .context import (init, init_local, stop, spark_context, default_reference, # noqa: E402
get_reference, set_global_seed, _set_flags, _get_flags, current_backend,
debug_info, citation, cite_hail, cite_hail_bibtex, version)
scan = agg.aggregators.ScanFunctions({name: getattr(agg, name) for name in agg.__all__})
__all__ = [
'init',
'init_local',
'stop',
'spark_context',
'default_reference',
'get_reference',
'set_global_seed',
'_set_flags',
'_get_flags',
'Table',
'GroupedTable',
'MatrixTable',
'GroupedMatrixTable',
'asc',
'desc',
'hadoop_open',
'hadoop_copy',
'hadoop_is_dir',
'hadoop_is_file',
'hadoop_stat',
'hadoop_exists',
'hadoop_ls',
'copy_log',
'Struct',
'Interval',
'agg',
'scan',
'genetics',
'methods',
'stats',
'linalg',
'nd',
'plot',
'experimental',
'ir',
'backend',
'current_backend',
'debug_info',
'citation',
'cite_hail',
'cite_hail_bibtex',
'version'
]
__all__.extend(genetics.__all__)
__all__.extend(methods.__all__)
# don't overwrite builtins in `from hail import *`
import builtins # noqa: E402
__all__.extend([x for x in expr.__all__ if not hasattr(builtins, x)])
del builtins
ir.register_functions()
ir.register_aggregators()
__version__ = None # set in hail.init()
import warnings # noqa: E402
warnings.filterwarnings('once', append=True)
del warnings
|
danking/hail
|
hail/python/hail/__init__.py
|
Python
|
mit
| 3,244
|
[
"VisIt"
] |
aef09b9a6fbf9db4d51d7972835b109a33b78904c57b53d32af49df86e5c276e
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
DOCUMENTATION = '''
---
version_added: "1.2"
module: jabber
short_description: Send a message to jabber user or chat room
description:
- Send a message to jabber
options:
user:
description:
User as which to connect
required: true
password:
description:
password for user to connect
required: true
to:
description:
user ID or name of the room, when using room use a slash to indicate your nick.
required: true
msg:
description:
- The message body.
required: true
default: null
host:
description:
host to connect, overrides user info
required: false
port:
description:
port to connect to, overrides default
required: false
default: 5222
encoding:
description:
message encoding
required: false
# informational: requirements for nodes
requirements: [ xmpp ]
author: Brian Coca
'''
EXAMPLES = '''
# send a message to a user
- jabber: user=mybot@example.net
password=secret
to=friend@example.net
msg="Ansible task finished"
# send a message to a room
- jabber: user=mybot@example.net
password=secret
to=mychaps@conference.example.net/ansiblebot
msg="Ansible task finished"
# send a message, specifying the host and port
- jabber user=mybot@example.net
host=talk.example.net
port=5223
password=secret
to=mychaps@example.net
msg="Ansible task finished"
'''
import os
import re
import time
HAS_XMPP = True
try:
import xmpp
except ImportError:
HAS_XMPP = False
def main():
module = AnsibleModule(
argument_spec=dict(
user=dict(required=True),
password=dict(required=True),
to=dict(required=True),
msg=dict(required=True),
host=dict(required=False),
port=dict(required=False,default=5222),
encoding=dict(required=False),
),
supports_check_mode=True
)
if not HAS_XMPP:
module.fail_json(msg="xmpp is not installed")
jid = xmpp.JID(module.params['user'])
user = jid.getNode()
server = jid.getDomain()
port = module.params['port']
password = module.params['password']
try:
to, nick = module.params['to'].split('/', 1)
except ValueError:
to, nick = module.params['to'], None
if module.params['host']:
host = module.params['host']
else:
host = server
if module.params['encoding']:
xmpp.simplexml.ENCODING = params['encoding']
msg = xmpp.protocol.Message(body=module.params['msg'])
try:
conn=xmpp.Client(server)
if not conn.connect(server=(host,port)):
module.fail_json(rc=1, msg='Failed to connect to server: %s' % (server))
if not conn.auth(user,password,'Ansible'):
module.fail_json(rc=1, msg='Failed to authorize %s on: %s' % (user,server))
# some old servers require this, also the sleep following send
conn.sendInitPresence(requestRoster=0)
if nick: # sending to room instead of user, need to join
msg.setType('groupchat')
msg.setTag('x', namespace='http://jabber.org/protocol/muc#user')
conn.send(xmpp.Presence(to=module.params['to']))
time.sleep(1)
else:
msg.setType('chat')
msg.setTo(to)
if not module.check_mode:
conn.send(msg)
time.sleep(1)
conn.disconnect()
except Exception, e:
module.fail_json(msg="unable to send msg: %s" % e)
module.exit_json(changed=False, to=to, user=user, msg=msg.getBody())
# import module snippets
from ansible.module_utils.basic import *
main()
|
hostmaster/ansible-modules-extras
|
notification/jabber.py
|
Python
|
gpl-3.0
| 3,778
|
[
"Brian"
] |
f58b093a39e19c71790fb92aca9f7d6eb2ca467ff502d08531444ffa8cb15f07
|
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
## \package pts.do.fitskirt.psf
# IMPORTANT: should be run after fitskirt_skysub
#
# This routine reads in a files list and a region list and determines the FWHM.
# The region list should be circles surrounding the stars used to determine the FWHM.
# Apart from the main function, functions have been copied from
# Sebastien Viaene's skysub.py script.
#
# REQUIREMENTS:
# - the files list should be free of ".fits" extension
# - the regions file should be made in ds9 and use circles saved as "image" or soatng
#
# OPTIONAL:
# - boolean for plotting the fitted result or not
#
# EXAMPLE: >pts fitskirt_psf files.dat stars.reg False
#
# This determines the FWHM for every star in stars.reg for all
# the images in files.dat and returns the average value.
#
# -----------------------------------------------------------------
# Import the necessary modules
import pyfits
import numpy as np
import itertools
import matplotlib.pyplot as plt
import sys
from scipy import optimize
from scipy.ndimage import interpolation
import matplotlib.pyplot as plt
from scipy.stats import nanmedian
from pylab import *
# -----------------------------------------------------------------
OK = '\033[92m'
ENDC = '\033[0m'
# Returns a 2D Gaussian distribution form the given parameters.
def gaussian(height, center_x, center_y, width_x, width_y):
"""Returns a gaussian function with the given parameters"""
width_x = float(width_x)
width_y = float(width_y)
return lambda x,y: height*exp(-(((center_x-x)/width_x)**2+((center_y-y)/width_y)**2)/2)
# Returns (height, x, y, width_x, width_y) the gaussian parameters of a 2D distribution by calculating its moments
def moments(data):
total = data.sum()
X, Y = indices(data.shape)
x = (X*data).sum()/total
y = (Y*data).sum()/total
col = data[:, int(y)]
width_x = sqrt(abs((arange(col.size)-y)**2*col).sum()/col.sum())
row = data[int(x), :]
width_y = sqrt(abs((arange(row.size)-x)**2*row).sum()/row.sum())
height = data.max()
return height, x, y, width_x, width_y
# Returns (height, x, y, width_x, width_y) the gaussian parameters of a 2D distribution found by a fit
def fitgaussian(data):
params = moments(data)
errorfunction = lambda p: ravel(gaussian(*p)(*indices(data.shape)) - data)
p, success = optimize.leastsq(errorfunction, params)
return p
# read the stars from the ds9 region and compute their central peak position through Gaussian fitting
def getStarPositions(frame,starRegion,plotting):
# Read the ds9 region of stars
reg_stars = open(starRegion,'r')
lines = reg_stars.readlines()
line = ''
xpos = 0
ypos = 0
rad = 0
stars = np.zeros((len(lines)-1,4))
# Loop over the lines, extract the region parameters and fit the stellar profiles with a 2D Gaussion
for l in range (1,len(lines)):
line = lines[l]
if "circ" in line:
line = line.replace('(',' ')
line = line.replace(')',' ')
line = line.replace(',',' ')
line = line.split(' ')
xpos = round(float(line[1]))
ypos = round(float(line[2]))
rad = round(float(line[3]))
# cut out a square around the star
square = np.zeros((2*rad,2*rad))
square = frame[ypos-rad:ypos+rad,xpos-rad:xpos+rad]
# fit a 2D Gaussian to the brightness distribution
params = fitgaussian(square)
fit = gaussian(*params)
(height, x, y, width_x, width_y) = params
# Plot the result
if plotting:
matshow(square, cmap=cm.CMRmap)
contour(fit(*indices(square.shape)), cmap=cm.Blues)
ax = gca()
text(0.95, 0.05, """
pxl max: %.1f
mod max: %.1f
x : %.1f
y : %.1f
width_x : %.1f
width_y : %.1f""" %(square[round(x),round(y)],height, x, y, width_x, width_y),
fontsize=16, horizontalalignment='right',color='white',
verticalalignment='bottom', transform=ax.transAxes)
show()
# Add the fitted parameters to the list of stars.
# NOTE: for some reason, x and y are interchanged by python.
stars[l-1,0] = xpos-rad+y
stars[l-1,1] = ypos-rad+x
stars[l-1,2] = width_y
stars[l-1,3] = width_x
return stars
# Main function, this part actually runs when routine is called
def main():
# Reading arguments from command
files = str(sys.argv[1])
regions = str(sys.argv[2])
plot = False
if len(sys.argv) > 3:
plot = str(sys.argv[3]) in ['true', 'True', '1', 't', 'y','yes']
# Read in frames file
f = open(files, 'r')
inputnames = f.read().splitlines()
nframes = len(inputnames)
# Loop over all frames and determine the FWHM
for i in range(0,nframes):
inputname = inputnames[i]+"_sub.fits"
hdulist = pyfits.open(inputname)
primhdr = pyfits.getheader(inputname, 0)
frame = hdulist[0].data
refstars = getStarPositions(frame,regions,plot)
aver_x, aver_y = 0.0, 0.0
for ref in refstars:
aver_x+=ref[2]
aver_y+=ref[3]
aver_x = aver_x/float(len(refstars))
aver_y = aver_y/float(len(refstars))
aver = (aver_x + aver_y)/2.0
print "\n "+OK+inputname+" has FWHM : "+str("{:5.2f}".format(aver))+ENDC+" ("+\
str("{:5.2f}".format(aver_x))+" in x-dir and "+str("{:5.2f}".format(aver_y))+" in y-dir )"
if __name__ == '__main__':
main()
|
Stargrazer82301/CAAPR
|
CAAPR/CAAPR_AstroMagic/PTS/pts/do/fitskirt/psf.py
|
Python
|
mit
| 5,502
|
[
"Gaussian"
] |
34409cbfe0fe33d55cc018a28d87f6aeef2601626b095cfaab13af77b3601264
|
#!/usr/bin/env python
#
# Wrapper script for starting the biopet-vcfstats JAR package
#
# This script is written for use with the Conda package manager and is copied
# from the peptide-shaker wrapper. Only the parameters are changed.
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py)
#
# This file was automatically generated by the sbt-bioconda plugin.
import os
import subprocess
import sys
import shutil
from os import access
from os import getenv
from os import X_OK
jar_file = 'VcfStats-assembly-1.0.jar'
default_jvm_mem_opts = []
# !!! End of parameter section. No user-serviceable code below this line !!!
def real_dirname(path):
"""Return the symlink-resolved, canonicalized directory-portion of path."""
return os.path.dirname(os.path.realpath(path))
def java_executable():
"""Return the executable name of the Java interpreter."""
java_home = getenv('JAVA_HOME')
java_bin = os.path.join('bin', 'java')
if java_home and access(os.path.join(java_home, java_bin), X_OK):
return os.path.join(java_home, java_bin)
else:
return 'java'
def jvm_opts(argv):
"""Construct list of Java arguments based on our argument list.
The argument list passed in argv must not include the script name.
The return value is a 3-tuple lists of strings of the form:
(memory_options, prop_options, passthrough_options)
"""
mem_opts = []
prop_opts = []
pass_args = []
exec_dir = None
for arg in argv:
if arg.startswith('-D'):
prop_opts.append(arg)
elif arg.startswith('-XX'):
prop_opts.append(arg)
elif arg.startswith('-Xm'):
mem_opts.append(arg)
elif arg.startswith('--exec_dir='):
exec_dir = arg.split('=')[1].strip('"').strip("'")
if not os.path.exists(exec_dir):
shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None)
else:
pass_args.append(arg)
# In the original shell script the test coded below read:
# if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]
# To reproduce the behaviour of the above shell code fragment
# it is important to explictly check for equality with None
# in the second condition, so a null envar value counts as True!
if mem_opts == [] and getenv('_JAVA_OPTIONS') is None:
mem_opts = default_jvm_mem_opts
return (mem_opts, prop_opts, pass_args, exec_dir)
def main():
"""
PeptideShaker updates files relative to the path of the jar file.
In a multiuser setting, the option --exec_dir="exec_dir"
can be used as the location for the peptide-shaker distribution.
If the exec_dir dies not exist,
we copy the jar file, lib, and resources to the exec_dir directory.
"""
java = java_executable()
(mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:])
jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0])
if pass_args != [] and pass_args[0].startswith('eu'):
jar_arg = '-cp'
else:
jar_arg = '-jar'
jar_path = os.path.join(jar_dir, jar_file)
java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args
sys.exit(subprocess.call(java_args))
if __name__ == '__main__':
main()
|
joachimwolff/bioconda-recipes
|
recipes/biopet-vcfstats/1.0/biopet-vcfstats.py
|
Python
|
mit
| 3,367
|
[
"Bioconda"
] |
af6ded4a66e1447f6cbd559ee73895b7ecb9fa6d5187f2598d9e531add774784
|
"""XOR Neural Net."""
import numpy as np
def sigmoid(x):
"""The Sigmoid Function."""
return 1 / (1 + np.exp(-x))
def NOT(x):
"""OR Neuron."""
fx = 10 - 20 * x
return sigmoid(fx)
def AND(x1, x2):
"""AND Neuron."""
fx = 20 * x1 + 20 * x2 - 30
return sigmoid(fx)
def OR(x1, x2):
"""OR Neuron."""
fx = 20 * x1 + 20 * x2 - 10
return sigmoid(fx)
def XORNN(x1, x2):
"""XOR Neural Net."""
return round(OR(AND(NOT(x1), x2), AND(x1, NOT(x2))))
print("0, 0 : " + str(XORNN(0, 0)))
print("0, 1 : " + str(XORNN(0, 1)))
print("1, 1 : " + str(XORNN(1, 1)))
print("1, 0 : " + str(XORNN(1, 0)))
|
rednithin/Misc-Mini
|
DeepLearning/XORNeuralNet.py
|
Python
|
gpl-3.0
| 643
|
[
"NEURON"
] |
5250cce688429c5fbf6f2a71cc312e1636ca9270d8c067f6c468c9754bd498f3
|
#!/usr/bin/env
"""
NARRuv_quiver_plot.py
"""
#System Stack
import datetime, sys
#Science Stack
from netCDF4 import Dataset, num2date
import numpy as np
# Visual Stack
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.dates import MonthLocator, DateFormatter
import matplotlib.ticker as ticker
__author__ = 'Shaun Bell'
__email__ = 'shaun.bell@noaa.gov'
__created__ = datetime.datetime(2016, 6, 20)
__modified__ = datetime.datetime(2016, 6, 20)
__version__ = "0.1.0"
__status__ = "Development"
__keywords__ = 'quiver plot'
"""-------------------------- Initialization params -----------------------------------------"""
### some mpl specif settings for fonts and plot style
mpl.rcParams['svg.fonttype'] = 'none'
plt.style.use('bmh')
"""--------------------------------netcdf Routines---------------------------------------"""
def get_global_atts(nchandle):
g_atts = {}
att_names = nchandle.ncattrs()
for name in att_names:
g_atts[name] = nchandle.getncattr(name)
return g_atts
def get_vars(nchandle):
return nchandle.variables
def get_var_atts(nchandle, var_name):
return nchandle.variables[var_name]
def ncreadfile_dic(nchandle, params):
data = {}
for j, v in enumerate(params):
if v in nchandle.variables.keys(): #check for nc variable
data[v] = nchandle.variables[v][:]
else: #if parameter doesn't exist fill the array with zeros
data[v] = None
return (data)
def data_ingest(file_name,subset_t, ucomp, vcomp):
### some data manipulation or massaging for plots
##
## generate daily averages from hourly data and label it 12Z of the day averaged
print file_name
nchandle = Dataset(file_name)
vars_dic = get_vars(nchandle)
data1 = ncreadfile_dic(nchandle,vars_dic.keys())
nchandle.close()
total_date_range = np.arange(data1["time"].min(),data1["time"].max(),1)
for count in total_date_range:
tind = (np.where(data1["time"] % count < 1))
try:
ucomp = np.hstack((ucomp, np.mean(data1['U_320'][tind,0,0,0])))
vcomp = np.hstack((vcomp, np.mean(data1['V_321'][tind,0,0,0])))
except:
ucomp = np.hstack((ucomp, np.mean(data1['u_1205'][tind,0,0,0])))
vcomp = np.hstack((vcomp, np.mean(data1['v_1206'][tind,0,0,0])))
subset_t = np.hstack((subset_t, count+0.5))
return (subset_t, ucomp, vcomp)
"""--------------------------------time Routines---------------------------------------"""
def date2pydate(file_time, file_time2=None, file_flag='EPIC'):
if file_flag == 'EPIC':
ref_time_py = datetime.datetime.toordinal(datetime.datetime(1968, 5, 23))
ref_time_epic = 2440000
offset = ref_time_epic - ref_time_py
try: #if input is an array
python_time = [None] * len(file_time)
for i, val in enumerate(file_time):
pyday = file_time[i] - offset
pyfrac = file_time2[i] / (1000. * 60. * 60.* 24.) #milliseconds in a day
python_time[i] = (pyday + pyfrac)
except:
pyday = file_time - offset
pyfrac = file_time2 / (1000. * 60. * 60.* 24.) #milliseconds in a day
python_time = (pyday + pyfrac)
else:
print "time flag not recognized"
sys.exit()
return np.array(python_time)
"""--------------------------------main Routines---------------------------------------"""
####The following is designed to plot U/V vecotrs from single depth adcp/rcm as a stick plot
### Read CF style netcdf files (one time word) from mulitple files
ncfiles = '/Volumes/WDC_internal/Users/bell/in_and_outbox/2016/stabeno/june/ArcticTransport/bottom_currents/'
site = 'C5/13ckp5a_wcp_vel_0038_brg_f35.cf.nc'
subset_t, ucomp, vcomp = [], [], []
(subset_t, ucomp, vcomp) = data_ingest(ncfiles+site,subset_t, ucomp, vcomp)
site = 'C5/14ckt5a_an9_0039m_brg_f35.cf.nc'
(subset_t, ucomp, vcomp) = data_ingest(ncfiles+site,subset_t, ucomp, vcomp)
xdate = num2date(subset_t, "days since 1800-01-01")
xdate = [x.toordinal() for x in xdate]
#exchange 1e35 for 0
ucomp[ucomp >= 1e34] = 0
vcomp[vcomp >= 1e34] = 0
###rotate
theta = np.deg2rad(-60) #effectively rotates axis ccw 60degrees
ucomp = ucomp*np.cos(theta) + vcomp*np.sin(theta)
vcomp = -ucomp*np.sin(theta) + vcomp*np.cos(theta)
magnitude = np.sqrt(ucomp**2 + vcomp**2)
### Quiver / Stick plot
# Plot quiver
fig = plt.figure(1)
for i in range(1,6):
ax1 = fig.add_subplot(5,1,i)
# 1D Quiver plot
q = ax1.quiver(xdate,0,ucomp,vcomp,color='r',units='y',scale_units='y',
scale = 1,headlength=2,headaxislength=2,width=0.6,alpha=.95)
qk = plt.quiverkey(q,0.2, 0.05, 5,r'$5 \frac{cm}{s}$',labelpos='W',
fontproperties={'weight': 'bold'})
ax1.set_ylim(vcomp.min(), vcomp.max())
ax1.set_ylim(vcomp.min(), vcomp.max())
ax1.set_ylabel("(cm/s)")
ax1.set_xlim(datetime.datetime(2010+i-1, 8, 01).toordinal(),datetime.datetime(2011+i-1, 10, 31).toordinal())
ax1.xaxis.set_major_locator(MonthLocator())
ax1.xaxis.set_minor_locator(MonthLocator(bymonth=range(1,13), bymonthday=15))
ax1.xaxis.set_major_formatter(ticker.NullFormatter())
ax1.xaxis.set_minor_formatter(DateFormatter('%b %y'))
ax1.tick_params(axis='both', which='minor', labelsize=12)
t = fig.suptitle('Daily Averaged Current', fontsize=12)
t.set_y(0.03)
fig.autofmt_xdate()
DefaultSize = fig.get_size_inches()
fig.set_size_inches( (DefaultSize[0]*2, DefaultSize[1]*1.50) )
plt.savefig('images/C5.png', bbox_inches='tight', dpi = (300))
plt.close()
#plt.show()
|
shaunwbell/FOCI_Analysis
|
general_plotting_routines/uv_quiver_plot.py
|
Python
|
mit
| 5,738
|
[
"NetCDF"
] |
9c3494f3bc1c70ec8c9412b3ce3bc5e72be82506745ae1a0cf0293f18ded9825
|
# Copyright 2013 the V8 project authors. All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Google Inc. nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import os
import shutil
import subprocess
import tarfile
from testrunner.local import testsuite
from testrunner.objects import testcase
class BenchmarksTestSuite(testsuite.TestSuite):
def __init__(self, name, root):
super(BenchmarksTestSuite, self).__init__(name, root)
self.testroot = root
def ListTests(self, context):
tests = []
for test in [
"kraken/ai-astar",
"kraken/audio-beat-detection",
"kraken/audio-dft",
"kraken/audio-fft",
"kraken/audio-oscillator",
"kraken/imaging-darkroom",
"kraken/imaging-desaturate",
"kraken/imaging-gaussian-blur",
"kraken/json-parse-financial",
"kraken/json-stringify-tinderbox",
"kraken/stanford-crypto-aes",
"kraken/stanford-crypto-ccm",
"kraken/stanford-crypto-pbkdf2",
"kraken/stanford-crypto-sha256-iterative",
"octane/box2d",
"octane/code-load",
"octane/crypto",
"octane/deltablue",
"octane/earley-boyer",
"octane/gbemu-part1",
"octane/mandreel",
"octane/navier-stokes",
"octane/pdfjs",
"octane/raytrace",
"octane/regexp",
"octane/richards",
"octane/splay",
"octane/typescript",
"octane/zlib",
"sunspider/3d-cube",
"sunspider/3d-morph",
"sunspider/3d-raytrace",
"sunspider/access-binary-trees",
"sunspider/access-fannkuch",
"sunspider/access-nbody",
"sunspider/access-nsieve",
"sunspider/bitops-3bit-bits-in-byte",
"sunspider/bitops-bits-in-byte",
"sunspider/bitops-bitwise-and",
"sunspider/bitops-nsieve-bits",
"sunspider/controlflow-recursive",
"sunspider/crypto-aes",
"sunspider/crypto-md5",
"sunspider/crypto-sha1",
"sunspider/date-format-tofte",
"sunspider/date-format-xparb",
"sunspider/math-cordic",
"sunspider/math-partial-sums",
"sunspider/math-spectral-norm",
"sunspider/regexp-dna",
"sunspider/string-base64",
"sunspider/string-fasta",
"sunspider/string-tagcloud",
"sunspider/string-unpack-code",
"sunspider/string-validate-input"]:
tests.append(testcase.TestCase(self, test))
return tests
def GetFlagsForTestCase(self, testcase, context):
result = []
result += context.mode_flags
if testcase.path.startswith("kraken"):
result.append(os.path.join(self.testroot, "%s-data.js" % testcase.path))
result.append(os.path.join(self.testroot, "%s.js" % testcase.path))
elif testcase.path.startswith("octane"):
result.append(os.path.join(self.testroot, "octane/base.js"))
result.append(os.path.join(self.testroot, "%s.js" % testcase.path))
if testcase.path.startswith("octane/gbemu"):
result.append(os.path.join(self.testroot, "octane/gbemu-part2.js"))
elif testcase.path.startswith("octane/typescript"):
result.append(os.path.join(self.testroot,
"octane/typescript-compiler.js"))
result.append(os.path.join(self.testroot, "octane/typescript-input.js"))
elif testcase.path.startswith("octane/zlib"):
result.append(os.path.join(self.testroot, "octane/zlib-data.js"))
result += ["-e", "BenchmarkSuite.RunSuites({});"]
elif testcase.path.startswith("sunspider"):
result.append(os.path.join(self.testroot, "%s.js" % testcase.path))
return testcase.flags + result
def GetSourceForTest(self, testcase):
filename = os.path.join(self.testroot, testcase.path + ".js")
with open(filename) as f:
return f.read()
def _DownloadIfNecessary(self, url, revision, target_dir):
# Maybe we're still up to date?
revision_file = "CHECKED_OUT_%s" % target_dir
checked_out_revision = None
if os.path.exists(revision_file):
with open(revision_file) as f:
checked_out_revision = f.read()
if checked_out_revision == revision:
return
# If we have a local archive file with the test data, extract it.
if os.path.exists(target_dir):
shutil.rmtree(target_dir)
archive_file = "downloaded_%s_%s.tar.gz" % (target_dir, revision)
if os.path.exists(archive_file):
with tarfile.open(archive_file, "r:gz") as tar:
tar.extractall()
with open(revision_file, "w") as f:
f.write(revision)
return
# No cached copy. Check out via SVN, and pack as .tar.gz for later use.
command = "svn co %s -r %s %s" % (url, revision, target_dir)
code = subprocess.call(command, shell=True)
if code != 0:
raise Exception("Error checking out %s benchmark" % target_dir)
with tarfile.open(archive_file, "w:gz") as tar:
tar.add("%s" % target_dir)
with open(revision_file, "w") as f:
f.write(revision)
def DownloadData(self):
old_cwd = os.getcwd()
os.chdir(os.path.abspath(self.root))
self._DownloadIfNecessary(
("http://svn.webkit.org/repository/webkit/trunk/PerformanceTests/"
"SunSpider/tests/sunspider-1.0.2/"),
"159499", "sunspider")
self._DownloadIfNecessary(
("http://kraken-mirror.googlecode.com/svn/trunk/kraken/tests/"
"kraken-1.1/"),
"8", "kraken")
self._DownloadIfNecessary(
"http://octane-benchmark.googlecode.com/svn/trunk/",
"26", "octane")
os.chdir(old_cwd)
def VariantFlags(self, testcase, default_flags):
# Both --nocrankshaft and --stressopt are very slow. Add TF but without
# always opt to match the way the benchmarks are run for performance
# testing.
return [[], ["--turbo-asm", "--turbo-filter=*"]]
def GetSuite(name, root):
return BenchmarksTestSuite(name, root)
|
KSanthanam/rethinkdb
|
external/v8_3.30.33.16/test/benchmarks/testcfg.py
|
Python
|
agpl-3.0
| 7,349
|
[
"Gaussian"
] |
92e5430202664a881bb94a9ddae3b333313d6fe74f2811825ff36df8debc0505
|
# -*- coding: utf-8 -*-
"""
Generators for geometric graphs.
"""
# Copyright (C) 2004-2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
__author__ = "\n".join(['Aric Hagberg (hagberg@lanl.gov)',
'Dan Schult (dschult@colgate.edu)',
'Ben Edwards (BJEdwards@gmail.com)'])
__all__ = ['random_geometric_graph',
'waxman_graph',
'geographical_threshold_graph',
'navigable_small_world_graph']
from bisect import bisect_left
from functools import reduce
from itertools import product
import math, random, sys
import networkx as nx
#---------------------------------------------------------------------------
# Random Geometric Graphs
#---------------------------------------------------------------------------
def random_geometric_graph(n, radius, dim=2, pos=None):
r"""Return the random geometric graph in the unit cube.
The random geometric graph model places n nodes uniformly at random
in the unit cube Two nodes `u,v` are connected with an edge if
`d(u,v)<=r` where `d` is the Euclidean distance and `r` is a radius
threshold.
Parameters
----------
n : int
Number of nodes
radius: float
Distance threshold value
dim : int, optional
Dimension of graph
pos : dict, optional
A dictionary keyed by node with node positions as values.
Returns
-------
Graph
Examples
--------
>>> G = nx.random_geometric_graph(20,0.1)
Notes
-----
This uses an `n^2` algorithm to build the graph. A faster algorithm
is possible using k-d trees.
The pos keyword can be used to specify node positions so you can create
an arbitrary distribution and domain for positions. If you need a distance
function other than Euclidean you'll have to hack the algorithm.
E.g to use a 2d Gaussian distribution of node positions with mean (0,0)
and std. dev. 2
>>> import random
>>> n=20
>>> p=dict((i,(random.gauss(0,2),random.gauss(0,2))) for i in range(n))
>>> G = nx.random_geometric_graph(n,0.2,pos=p)
References
----------
.. [1] Penrose, Mathew, Random Geometric Graphs,
Oxford Studies in Probability, 5, 2003.
"""
G=nx.Graph()
G.name="Random Geometric Graph"
G.add_nodes_from(range(n))
if pos is None:
# random positions
for n in G:
G.node[n]['pos']=[random.random() for i in range(0,dim)]
else:
nx.set_node_attributes(G,'pos',pos)
# connect nodes within "radius" of each other
# n^2 algorithm, could use a k-d tree implementation
nodes = G.nodes(data=True)
while nodes:
u,du = nodes.pop()
pu = du['pos']
for v,dv in nodes:
pv = dv['pos']
d = sum(((a-b)**2 for a,b in zip(pu,pv)))
if d <= radius**2:
G.add_edge(u,v)
return G
def geographical_threshold_graph(n, theta, alpha=2, dim=2,
pos=None, weight=None):
r"""Return a geographical threshold graph.
The geographical threshold graph model places n nodes uniformly at random
in a rectangular domain. Each node `u` is assigned a weight `w_u`.
Two nodes `u,v` are connected with an edge if
.. math::
w_u + w_v \ge \theta r^{\alpha}
where `r` is the Euclidean distance between `u` and `v`,
and `\theta`, `\alpha` are parameters.
Parameters
----------
n : int
Number of nodes
theta: float
Threshold value
alpha: float, optional
Exponent of distance function
dim : int, optional
Dimension of graph
pos : dict
Node positions as a dictionary of tuples keyed by node.
weight : dict
Node weights as a dictionary of numbers keyed by node.
Returns
-------
Graph
Examples
--------
>>> G = nx.geographical_threshold_graph(20,50)
Notes
-----
If weights are not specified they are assigned to nodes by drawing randomly
from an the exponential distribution with rate parameter `\lambda=1`.
To specify a weights from a different distribution assign them to a
dictionary and pass it as the weight= keyword
>>> import random
>>> n = 20
>>> w=dict((i,random.expovariate(5.0)) for i in range(n))
>>> G = nx.geographical_threshold_graph(20,50,weight=w)
If node positions are not specified they are randomly assigned from the
uniform distribution.
References
----------
.. [1] Masuda, N., Miwa, H., Konno, N.:
Geographical threshold graphs with small-world and scale-free properties.
Physical Review E 71, 036108 (2005)
.. [2] Milan Bradonjić, Aric Hagberg and Allon G. Percus,
Giant component and connectivity in geographical threshold graphs,
in Algorithms and Models for the Web-Graph (WAW 2007),
Antony Bonato and Fan Chung (Eds), pp. 209--216, 2007
"""
G=nx.Graph()
# add n nodes
G.add_nodes_from([v for v in range(n)])
if weight is None:
# choose weights from exponential distribution
for n in G:
G.node[n]['weight'] = random.expovariate(1.0)
else:
nx.set_node_attributes(G,'weight',weight)
if pos is None:
# random positions
for n in G:
G.node[n]['pos']=[random.random() for i in range(0,dim)]
else:
nx.set_node_attributes(G,'pos',pos)
G.add_edges_from(geographical_threshold_edges(G, theta, alpha))
return G
def geographical_threshold_edges(G, theta, alpha=2):
# generate edges for a geographical threshold graph given a graph
# with positions and weights assigned as node attributes 'pos' and 'weight'.
nodes = G.nodes(data=True)
while nodes:
u,du = nodes.pop()
wu = du['weight']
pu = du['pos']
for v,dv in nodes:
wv = dv['weight']
pv = dv['pos']
r = math.sqrt(sum(((a-b)**2 for a,b in zip(pu,pv))))
if wu+wv >= theta*r**alpha:
yield(u,v)
def waxman_graph(n, alpha=0.4, beta=0.1, L=None, domain=(0,0,1,1)):
r"""Return a Waxman random graph.
The Waxman random graph models place n nodes uniformly at random
in a rectangular domain. Two nodes u,v are connected with an edge
with probability
.. math::
p = \alpha*exp(-d/(\beta*L)).
This function implements both Waxman models.
Waxman-1: `L` not specified
The distance `d` is the Euclidean distance between the nodes u and v.
`L` is the maximum distance between all nodes in the graph.
Waxman-2: `L` specified
The distance `d` is chosen randomly in `[0,L]`.
Parameters
----------
n : int
Number of nodes
alpha: float
Model parameter
beta: float
Model parameter
L : float, optional
Maximum distance between nodes. If not specified the actual distance
is calculated.
domain : tuple of numbers, optional
Domain size (xmin, ymin, xmax, ymax)
Returns
-------
G: Graph
References
----------
.. [1] B. M. Waxman, Routing of multipoint connections.
IEEE J. Select. Areas Commun. 6(9),(1988) 1617-1622.
"""
# build graph of n nodes with random positions in the unit square
G = nx.Graph()
G.add_nodes_from(range(n))
(xmin,ymin,xmax,ymax)=domain
for n in G:
G.node[n]['pos']=((xmin + (xmax-xmin))*random.random(),
(ymin + (ymax-ymin))*random.random())
if L is None:
# find maximum distance L between two nodes
l = 0
pos = list(nx.get_node_attributes(G,'pos').values())
while pos:
x1,y1 = pos.pop()
for x2,y2 in pos:
r2 = (x1-x2)**2 + (y1-y2)**2
if r2 > l:
l = r2
l=math.sqrt(l)
else:
# user specified maximum distance
l = L
nodes=G.nodes()
if L is None:
# Waxman-1 model
# try all pairs, connect randomly based on euclidean distance
while nodes:
u = nodes.pop()
x1,y1 = G.node[u]['pos']
for v in nodes:
x2,y2 = G.node[v]['pos']
r = math.sqrt((x1-x2)**2 + (y1-y2)**2)
if random.random() < alpha*math.exp(-r/(beta*l)):
G.add_edge(u,v)
else:
# Waxman-2 model
# try all pairs, connect randomly based on randomly chosen l
while nodes:
u = nodes.pop()
for v in nodes:
r = random.random()*l
if random.random() < alpha*math.exp(-r/(beta*l)):
G.add_edge(u,v)
return G
def navigable_small_world_graph(n, p=1, q=1, r=2, dim=2, seed=None):
r"""Return a navigable small-world graph.
A navigable small-world graph is a directed grid with additional
long-range connections that are chosen randomly. From [1]_:
Begin with a set of nodes that are identified with the set of lattice
points in an `n \times n` square, `{(i,j): i\in {1,2,\ldots,n}, j\in {1,2,\ldots,n}}`
and define the lattice distance between two nodes `(i,j)` and `(k,l)`
to be the number of "lattice steps" separating them: `d((i,j),(k,l)) = |k-i|+|l-j|`.
For a universal constant `p`, the node `u` has a directed edge to every other
node within lattice distance `p` (local contacts) .
For universal constants `q\ge 0` and `r\ge 0` construct directed edges from `u` to `q`
other nodes (long-range contacts) using independent random trials; the i'th
directed edge from `u` has endpoint `v` with probability proportional to `d(u,v)^{-r}`.
Parameters
----------
n : int
The number of nodes.
p : int
The diameter of short range connections. Each node is connected
to every other node within lattice distance p.
q : int
The number of long-range connections for each node.
r : float
Exponent for decaying probability of connections. The probability of
connecting to a node at lattice distance d is 1/d^r.
dim : int
Dimension of grid
seed : int, optional
Seed for random number generator (default=None).
References
----------
.. [1] J. Kleinberg. The small-world phenomenon: An algorithmic
perspective. Proc. 32nd ACM Symposium on Theory of Computing, 2000.
"""
if (p < 1):
raise nx.NetworkXException("p must be >= 1")
if (q < 0):
raise nx.NetworkXException("q must be >= 0")
if (r < 0):
raise nx.NetworkXException("r must be >= 1")
if not seed is None:
random.seed(seed)
G = nx.DiGraph()
nodes = list(product(range(n),repeat=dim))
for p1 in nodes:
probs = [0]
for p2 in nodes:
if p1==p2:
continue
d = sum((abs(b-a) for a,b in zip(p1,p2)))
if d <= p:
G.add_edge(p1,p2)
probs.append(d**-r)
cdf = list(nx.utils.cumulative_sum(probs))
for _ in range(q):
target = nodes[bisect_left(cdf,random.uniform(0, cdf[-1]))]
G.add_edge(p1,target)
return G
|
aitoralmeida/networkx
|
networkx/generators/geometric.py
|
Python
|
bsd-3-clause
| 11,379
|
[
"Gaussian"
] |
acb1d7ca6ead522a76da6365b1e4774ad48f61663461ea7db309cb5a70bf2e40
|
#!/usr/bin/env python
import os
import sys
import subprocess as sp
import argparse
if sys.version_info.major == 3:
PY3 = True
from urllib.request import urlretrieve
else:
PY3 = True
from urllib import urlretrieve
usage = """
The easy way to test recipes is by using `circleci build`. However this does
not allow local testing recipes using mulled-build (due to the technicalities
of running docker within docker and the CircleCI client).
This script makes it easy to do mulled-build tests. It works by using the same
code used in the .circleci/setup.sh script to build an isolated Miniconda
environment and a custom `activate` script.
Set up the environment like this:
./bootstrap.py /tmp/miniconda
It creates an activate script at ~/.config/bioconda/activate. So you can then use:
source ~/.config/bioconda/activate
and then use that isolated root environment independent of any other conda
installations you might have.
"""
ap = argparse.ArgumentParser(usage)
ap.add_argument('bootstrap', help='''Location to which a new Miniconda
installation plus bioconda-utils should be installed. This will
be separate from any existing conda installations.''')
ap.add_argument('--no-docker', action='store_true', help='''By default we
expect Docker to be present. Use this arg to disable that
behavior. This will reduce functionality, but is useful if
you're unable to install docker.''')
args = ap.parse_args()
# This is the "common" step in the CircleCI config which gets the versions of
# Miniconda and bioconda-utils that we're using.
urlretrieve(
'https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh',
filename='.circleci/common.sh')
# TODO: this mimics the override in the "common" job in .circleci/config.yaml
with open('.circleci/common.sh', 'w') as fout:
fout.write("MINICONDA_VER=py37_4.8.3\nBIOCONDA_UTILS_TAG=master\n")
local_config_path = os.path.expanduser('~/.config/bioconda/activate')
def _write_custom_activate(install_path):
"""
Once the isolated Miniconda version has been installed, copy its activate
script over to a custom location, and then hard-code the paths and PS1. We
don't need a matching `deactivate` because the activate script properly
keeps track of the new location.
"""
config_dir = os.path.dirname(local_config_path)
if not os.path.exists(config_dir):
os.makedirs(config_dir)
activate = os.path.join(install_path, 'miniconda/bin/activate')
lines = [i.rstrip() for i in open(activate)]
# The following is code from cb2; disabling but keeping it around for now:
if 0:
# Exact matches to lines we want to replace in the activate script, leading
# space included.
substitutions = [
(
'_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")',
'_CONDA_DIR="{0}/miniconda/bin"'.format(install_path)
),
(
' export PS1="(${CONDA_DEFAULT_ENV}) $PS1"',
' export PS1="(BIOCONDA-UTILS) $PS1"',
)
]
for orig, sub in substitutions:
# Be very picky so that we'll know if/when the activate script changes.
try:
pos = lines.index(orig)
except ValueError:
raise ValueError(
"Expecting '{0}' to be in {1} but couldn't find it"
.format(orig, activate)
)
lines[pos] = sub
with open(local_config_path, 'w') as fout:
for line in lines:
fout.write(line + '\n')
use_docker = "true"
if args.no_docker:
use_docker = "false"
env = {
'WORKSPACE': args.bootstrap,
'BOOTSTRAP': "true",
'USE_DOCKER': use_docker,
'PATH': os.environ.get('PATH', ""),
'HTTPS_PROXY': os.environ.get('HTTPS_PROXY', ""),
'https_proxy': os.environ.get('https_proxy', "")
}
sp.check_call(['.circleci/setup.sh'], env=env)
_write_custom_activate(args.bootstrap)
print("""
An isolated version of bioconda-utils has been installed to {1}. This is
separate from any other conda installations you might have.
To use it, source this custom activate script:
source ~/.config/bioconda/activate
When done:
source deactivate
""")
|
ostrokach/bioconda-recipes
|
bootstrap.py
|
Python
|
mit
| 4,385
|
[
"Bioconda"
] |
a7158b7c80f20662bfac390ac79fe8513dd0fa3164031fe0716444735f2dd2bb
|
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 2 as published by
# the Free Software Foundation.
#
# For complete information please visit: http://www.zenoss.com/oss/
#
###########################################################################
import re
import logging
from Products.ZenRRD.CommandParser import CommandParser
log = logging.getLogger("zen.zencommand")
"""
Items to collect:
coolingStatus
enclosureStatus
OAStatus
powerAvailableDC
powerCapacityDC
powerPresentAC
powerStatus
"""
class EnclosureStatus(CommandParser):
def processResults(self, cmd, result):
"""
Parse the results of the "SHOW ENCLOSURE STATUS" command
to get details about power usage and component status.
"""
output = cmd.result.output
dps = dict([(dp.id, dp) for dp in cmd.points])
outlines = output.split('\n')
log.debug("EnclosureStatusParser: I have %d lines to parse" % len(outlines))
for i, line in enumerate(outlines):
if "Enclosure" in line:
if "OK" in outlines[i+1]:
result.values.append( (dps["enclosureStatus"], float(0)) )
else:
result.values.append( (dps["enclosureStatus"], float(1)) )
if "Onboard Administrator" in line:
if "OK" in outlines[i+1]:
result.values.append( (dps["OAStatus"], float(0)) )
else:
result.values.append( (dps["OAStatus"], float(1)) )
if "Power Subsystem" in line:
if "OK" in outlines[i+1]:
result.values.append( (dps["powerStatus"], float(0)) )
else:
result.values.append( (dps["powerStatus"], float(1)) )
if "Power" in line:
log.debug("EnclosureStatusParser: Found line with Power in it: %s" % line)
match = re.match("^([^:]+):.([0-9]+).Watts.*$", line.strip())
if match:
log.debug("EnclosureStatusParser: Found line to match the regex: %s" % line)
(key, value) = match.groups()
if "Power Capacity" in key:
result.values.append( (dps["powerCapacityDC"], float(value)) )
if "Power Available" in key:
result.values.append( (dps["powerAvailableDC"], float(value)) )
if "Present Power" in key:
result.values.append( (dps["powerPresentAC"], float(value)) )
if "Cooling Subsystem" in line:
if "OK" in outlines[i+1]:
result.values.append( (dps["coolingStatus"], float(0)) )
else:
result.values.append( (dps["coolingStatus"], float(1)) )
return result
|
zenoss/ZenPacks.community.HPBladeChassis
|
ZenPacks/community/HPBladeChassis/parsers/HPBladeChassis/EnclosureStatus.py
|
Python
|
gpl-2.0
| 3,122
|
[
"VisIt"
] |
4acd9a6bbac7f3da05ff5f847074d37cdd816df587c82b60a1abb59836d4ea08
|
from __future__ import absolute_import # Need to import pulsar_client absolutely.
from ..objectstore import ObjectStore
from pulsar.client.manager import ObjectStoreClientManager
class PulsarObjectStore(ObjectStore):
"""
Object store implementation that delegates to a remote Pulsar server.
This may be more aspirational than practical for now, it would be good to
Galaxy to a point that a handler thread could be setup that doesn't attempt
to access the disk files returned by a (this) object store - just passing
them along to the Pulsar unmodified. That modification - along with this
implementation and Pulsar job destinations would then allow Galaxy to fully
manage jobs on remote servers with completely different mount points.
This implementation should be considered beta and may be dropped from
Galaxy at some future point or significantly modified.
"""
def __init__(self, config, config_xml):
self.pulsar_client = self.__build_pulsar_client(config_xml)
def exists(self, obj, **kwds):
return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds))
def file_ready(self, obj, **kwds):
return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds))
def create(self, obj, **kwds):
return self.pulsar_client.create(**self.__build_kwds(obj, **kwds))
def empty(self, obj, **kwds):
return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds))
def size(self, obj, **kwds):
return self.pulsar_client.size(**self.__build_kwds(obj, **kwds))
def delete(self, obj, **kwds):
return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds))
# TODO: Optimize get_data.
def get_data(self, obj, **kwds):
return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds))
def get_filename(self, obj, **kwds):
return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds))
def update_from_file(self, obj, **kwds):
return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds))
def get_store_usage_percent(self):
return self.pulsar_client.get_store_usage_percent()
def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
return None
def __build_kwds(self, obj, **kwds):
kwds['object_id'] = obj.id
return kwds
pass
def __build_pulsar_client(self, config_xml):
url = config_xml.get("url")
private_token = config_xml.get("private_token", None)
transport = config_xml.get("transport", None)
manager_options = dict(transport=transport)
client_options = dict(url=url, private_token=private_token)
pulsar_client = ObjectStoreClientManager(**manager_options).get_client(client_options)
return pulsar_client
def shutdown(self):
pass
|
ssorgatem/pulsar
|
galaxy/objectstore/pulsar.py
|
Python
|
apache-2.0
| 2,899
|
[
"Galaxy"
] |
1d525388b6cf9e35e4abff59868e30aa9d7eb4be795038056fe585cec2e809fa
|
import os
import zipfile
import io
from django.views.generic import View, ListView, CreateView, UpdateView, DeleteView, DetailView
from django.shortcuts import render, render_to_response, get_object_or_404
from django.contrib.auth import authenticate, login, logout
from django.contrib.auth.models import Group, User
from django.http import HttpResponseRedirect, HttpResponse
from django.core.urlresolvers import reverse
from django.db.models import Q
from django.core.mail import send_mail
from django.core.context_processors import csrf
from django.utils import timezone
from django.template import RequestContext
from secure_witness.models import *
from secure_witness.forms import *
import hashlib, datetime, random
from Crypto.Cipher import DES3
import random
import mimetypes
from django.http import JsonResponse
import json
from django.views.decorators.csrf import csrf_exempt
def search(request):
query = request.GET.get('q')
q = Q(private=False) | Q(created_by=request.user)
user_group_list = request.user.groups.all()
for g in user_group_list:
q |= Q(authorized_groups=g)
if query:
results = Report.objects.filter(q, Q(short__icontains=query) | Q(detailed__icontains=query) | Q(keywords__icontains=query)).order_by('time')
else:
results = Report.objects.filter(q)
return render(request, 'search_result.html', {'results':results})
def saved(request):
return HttpResponse("saved")
def copy(request, pk):
fld = Report.objects.get(id=pk)
fld.pk = None
fld.id = None
fld.save()
return HttpResponseRedirect(reverse('report-detail', args=(fld.id,)))
def advanced_search(request):
if request.method == 'POST':
short = request.POST.get('short_description')
detailed = request.POST.get('detailed_description')
keyword = request.POST.get('keywords')
user_group_list = request.user.groups.all()
query = Q(private=False) | Q(created_by=request.user)
for g in user_group_list:
query |= Q(authorized_groups=g)
if short or detailed or keyword:
results = Report.objects.filter(query, short__icontains=short, detailed__icontains=detailed, keywords__icontains=keyword).order_by('time')
else:
results = Report.objects.filter(query)
return render(request, 'search_result.html', {'results':results})
else:
return render(request, 'advanced_search.html', {})
class JointFolderReportView(View):
def get(self, request, folder_id):
if folder_id:
# Load reports in a specific folder
folder_list = []
# Only retrieve public reports or ones that the user owns
user_group_list = request.user.groups.all()
query = Q(private=False) | Q(created_by=self.request.user)
for g in user_group_list:
query |= Q(authorized_groups=g)
report_list = Report.objects.filter(Q(folder__id=folder_id), query).distinct().order_by('short')
cur_folder_name = Folder.objects.filter(id=folder_id)[0].folder_name
else:
# Load all folders and reports
folder_list = Folder.objects.all().order_by('folder_name')
# Only retrieve public reports or ones that the user owns
user_group_list = request.user.groups.all()
query = Q(private=False) | Q(created_by=self.request.user)
for g in user_group_list:
query |= Q(authorized_groups=g)
report_list = Report.objects.filter(Q(folder__id=None), query).order_by('short')
cur_folder_name = None
# Render the page with the appropriate data
return render(request, 'combined_folder_report_list.html', {
'folder_list': folder_list,
'report_list': report_list,
'cur_folder_name': cur_folder_name,
})
class CreateReportView(CreateView):
model = Report
template_name = 'report_edit.html'
form_class = ReportForm
def form_valid(self, form):
form.instance.created_by = self.request.user
form.instance.updated_by = self.request.user
return super(CreateReportView, self).form_valid(form)
def get_success_url(self):
# Save each file associated with the report
# Save each file associated with the report
for file in self.request.FILES.getlist('files'):
mimetypes.init()
mime_type = mimetypes.guess_type(str(file))
file_type = mime_type[0]
if self.object.private:
new_iv = ''.join(random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ') for i in range(8))
new_key = ''.join(random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ') for j in range(16))
des3 = DES3.new(new_key, DES3.MODE_CFB, new_iv)
enc_filename = str(file) + ".enc"
with open("media/" + enc_filename, 'wb') as enc_file:
for chunk in file.chunks(8192):
if len(chunk) == 0:
break
elif len(chunk) % 16 != 0:
chunk += (' ' * (16 - len(chunk) % 16)).encode()
enc_file.write(des3.encrypt(chunk))
else:
enc_file.write(des3.encrypt(chunk))
enc_file.seek(0)
m = Media(filename=str(enc_filename), is_encrypted=self.object.private, content=enc_filename,
report=self.object, key=new_key, iv=new_iv, fileType=file_type,
created_by=self.request.user, updated_by=self.request.user)
m.save()
else:
m = Media(filename=str(file), is_encrypted=self.object.private, content=file,
report=self.object, fileType=file_type,
created_by=self.request.user, updated_by=self.request.user)
m.save()
# Every report can be seen by admins
admin_group = Group.objects.get(name="admins")
self.object.authorized_groups.add(admin_group)
# Get the folder id from the object for the reverse url
if self.object.folder:
return reverse('browse', args=(self.object.folder.id,))
else:
return reverse('browse')
def get_context_data(self, **kwargs):
context = super(CreateReportView, self).get_context_data(**kwargs)
context['action'] = reverse('reports-new')
return context
class UpdateReportView(UpdateView):
model = Report
template_name = 'report_edit.html'
form_class = ReportForm
def form_valid(self, form):
form.instance.updated_by = self.request.user
return super(UpdateReportView, self).form_valid(form)
def get_success_url(self):
# Save each file associated with the report
# Save each file associated with the report
for file in self.request.FILES.getlist('files'):
mimetypes.init()
mime_type = mimetypes.guess_type(str(file))
file_type = mime_type[0]
if self.object.private:
new_iv = ''.join(random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ') for i in range(8))
new_key = ''.join(random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ') for j in range(16))
des3 = DES3.new(new_key, DES3.MODE_CFB, new_iv)
enc_filename = str(file) + ".enc"
with open("media/" + enc_filename, 'wb') as enc_file:
for chunk in file.chunks(8192):
if len(chunk) == 0:
break
elif len(chunk) % 16 != 0:
chunk += (' ' * (16 - len(chunk) % 16)).encode()
enc_file.write(des3.encrypt(chunk))
else:
enc_file.write(des3.encrypt(chunk))
enc_file.seek(0)
m = Media(filename=str(enc_filename), is_encrypted=self.object.private, content=enc_filename,
report=self.object, key=new_key, iv=new_iv, fileType=file_type,
created_by=self.request.user, updated_by=self.request.user)
m.save()
else:
m = Media(filename=str(file), is_encrypted=self.object.private, content=file,
report=self.object, fileType=file_type,
created_by=self.request.user, updated_by=self.request.user)
m.save()
# Every report can be seen by admins
admin_group = Group.objects.get(name="admins")
self.object.authorized_groups.add(admin_group)
# Get the folder id from the object for the reverse url
if self.object.folder:
return reverse('browse', args=(self.object.folder.id,))
else:
return reverse('browse')
def get_context_data(self, **kwargs):
context = super(UpdateReportView, self).get_context_data(**kwargs)
context['action'] = reverse('report-edit', kwargs={'pk': self.get_object().id})
context['file_list'] = Media.objects.filter(report__id=self.object.id)
return context
class DeleteReportView(DeleteView):
model = Report
template_name = 'delete_report.html'
def get_success_url(self):
if self.object.folder:
return reverse('browse', args=(self.object.folder.id,))
else:
return reverse('browse')
class ReportView(DetailView):
model = Report
template_name = 'report.html'
def get_context_data(self, **kwargs):
context = super(ReportView, self).get_context_data(**kwargs)
context['file_list'] = Media.objects.filter(report__id=self.object.id)
# Get the list of comments associated with the report
context['comment_list'] = Comment.objects.filter(report__id=self.object.id).order_by('-created_at')
return context
class CreateFolderView(CreateView):
model = Folder
fields = "__all__"
template_name = 'edit_folder.html'
def form_valid(self, form):
form.instance.created_by = self.request.user
form.instance.updated_by = self.request.user
return super(CreateFolderView, self).form_valid(form)
def get_success_url(self):
return reverse('browse')
def get_context_data(self, **kwargs):
context = super(CreateFolderView, self).get_context_data(**kwargs)
context['action'] = reverse('folders-new')
return context
class UpdateFolderView(UpdateView):
model = Folder
fields = "__all__"
template_name = 'edit_folder.html'
def form_valid(self, form):
form.instance.updated_by = self.request.user
return super(UpdateFolderView, self).form_valid(form)
def get_success_url(self):
return reverse('browse')
def get_context_data(self, **kwargs):
context = super(UpdateFolderView, self).get_context_data(**kwargs)
context['action'] = reverse('folders-edit',
kwargs={'pk': self.get_object().id})
return context
class DeleteFolderView(DeleteView):
model = Folder
fields = "__all__"
template_name = 'delete_folder.html'
def get_success_url(self):
return reverse('browse')
class FolderView(DetailView):
model = Folder
fields = "__all__"
template_name = 'folder.html'
def user_login(request):
# Process data from POST
print('Request received')
if request.method == 'POST':
print("post-received")
# User .get() method to return None if not present
username = request.POST.get('username')
password = request.POST.get('password')
# Check if password is valid
user = authenticate(username=username, password=password)
# If user != None, then login worked
if user:
if user.is_active:
login(request, user)
# Link to the post-login screen
return HttpResponseRedirect('/browse/')
else:
return HttpResponse("Account is disabled. Please contact the admin.")
# Login not successful
else:
print("Invalid login details: {0}, {1}".format(username, password))
return HttpResponse("Invalid login information supplied")
# GET request, create a blank form
else:
return render(request, 'login.html', {})
def user_logout(request):
# User must be logged in to reach this section, so can just logout
logout(request)
return HttpResponseRedirect('/login/')
def register_user(request):
args = {}
args.update(csrf(request))
if request.method == 'POST':
form = RegistrationForm(request.POST)
args['form'] = form
if form.is_valid():
form.save()
username = form.cleaned_data['username']
email = form.cleaned_data['email']
random_string = str(random.random()).encode('utf8')
salt = hashlib.sha1(random_string).hexdigest()[:5]
salted = (salt + email).encode('utf8')
activation_key = hashlib.sha1(salted).hexdigest()
key_expires = timezone.now() + datetime.timedelta(2)
# Get the user
user = User.objects.get(username=username)
# Create new user profile
user_profile = UserProfile(user=user, activation_key=activation_key,
key_expires=key_expires)
user_profile.save()
# Send activation email
email_subject = 'Account Confirmation'
email_body = "To activate your account, please visit: \
/confirm/%s" % (activation_key)
send_mail(email_subject, email_body, 'g19securewitness@gmail.com', [email], fail_silently=False)
return HttpResponseRedirect('login')
else:
args['form'] = RegistrationForm()
return render_to_response('register.html', args, context_instance=RequestContext(request))
def register_confirm(request, activation_key):
# If the user is already logged in, stop activation process
if request.user.is_authenticated():
HttpResponseRedirect('/browse')
# Check if a user with the activation_key exists
user_profile = get_object_or_404(UserProfile, activation_key=activation_key)
# Make sure the user has not expired
if user_profile.key_expires < timezone.now():
return HttpResponse("Activation key has expired. Please re-register")
user = user_profile.user
user.is_active = True
user.save()
return HttpResponse("Account confirmed")
class GroupListView(ListView):
context_object_name = "group_list"
template_name = "group_list.html"
def get_queryset(self):
user = self.request.user
if user.groups.filter(name='admins').exists():
return Group.objects.all()
else:
return self.request.user.groups.all()
class GroupDetailView(DetailView):
model = Group
context_object_name = "group"
template_name = "group_detail.html"
def get_context_data(self, **kwargs):
context = super(GroupDetailView, self).get_context_data(**kwargs)
context['user_list'] = self.object.user_set.all()
return context
class GroupEditView(UpdateView):
model = Group
context_object_name = "group"
template_name = 'group_edit.html'
fields = ['name']
def get_success_url(self):
return reverse('group-list')
def get_context_data(self, **kwargs):
context = super(GroupEditView, self).get_context_data(**kwargs)
context['user_list'] = self.object.user_set.all()
return context
class GroupDeleteView(DeleteView):
model = Group
template_name = 'group_confirm_delete.html'
def get_success_url(self):
return reverse('group-list')
class GroupCreateView(CreateView):
model = Group
fields = ['name']
template_name = 'group_edit.html'
def get_success_url(self):
return reverse('group-list')
def form_valid(self, form):
# Add the current user to the group
g = form.save()
g.user_set.add(self.request.user)
g.save()
return super(GroupCreateView, self).form_valid(form)
def add_user(request, group_id):
if request.method == 'POST':
# Get the username from the request
username = request.POST.get('username')
# Retrieve user object with the specified username
user_list = User.objects.filter(username=username)
# If user with username exists, add them to the current group
if len(user_list) > 0:
user = user_list[0]
group_id = int(group_id)
g = Group.objects.get(id=group_id)
g.user_set.add(user)
else:
# TODO HANDLE ERRORS
print("User not found")
# Return to the group-edit page
return HttpResponseRedirect(reverse('group-edit', args=(group_id,)))
def remove_user(request, group_id, user_id):
group_id = int(group_id)
user_id = int(user_id)
# Remove the user from the group
g = Group.objects.get(id=group_id)
u = User.objects.get(id=user_id)
g.user_set.remove(u)
return HttpResponseRedirect(reverse('group-edit', args=(group_id,)))
class AdminUserManager(View):
def get(self, request):
# Load the users onto the page
user_list = User.objects.all().order_by('username')
return render(request, 'user_manager_list.html', {
'user_list': user_list,
})
def switch_user_active(request, user_id):
user_id = int(user_id)
user = User.objects.get(id=user_id)
user.is_active = (not user.is_active)
user.save()
return HttpResponseRedirect('/user-manager/')
def edit_profile(request):
#Save the new info into the existing user instance
if request.method == "POST":
form = UserForm(data=request.POST, instance=request.user)
if form.is_valid():
user = form.save(commit=False)
user.set_password(user.password)
user.save()
#else:
# return HttpResponse("Please enter information for each field.")
#Keep the user logged in
# User .get() method to return None if not present
username = request.POST.get('username')
password = request.POST.get('password')
# Check if password is valid
sameuser = authenticate(username=username, password=password)
# If user != None, then login worked
if sameuser:
if sameuser.is_active:
login(request, sameuser)
# Link to the post-login screen
return HttpResponseRedirect('/browse/')
else:
return HttpResponse("Account is disabled. Please contact the admin.")
else:
return HttpResponse("Invalid login information supplied")
#display the edit form with existing user instance information
else:
form = UserForm(instance=request.user)
return render(request, 'edit_profile.html', {'form': form})
def downloadfiles(request, pk):
# Files (local path) to put in the .zip
# FIXME: Change this (get paths from DB etc)
filenames = []
if Media.objects.filter(id=pk):
for querydict in Media.objects.filter(id=pk).values():
path = '/cs3240-s15-team19/group/media/'+querydict[filename]
if path != '':
filenames.append(path)
for querydict in Media.objects.filter(id=pk).values():
path = '/cs3240-s15-team19/group/media/'+querydict['filename']
if path != '':
filenames.append(path)
# The zip compressor
zf = zipfile.ZipFile('media.zip', "w")
for x in filenames:
zf.write(x)
# Must close zip for all contents to be written
zf.close()
# Grab ZIP file from in-memory
resp = HttpResponse(zf, content_type='application/zip')
# ..and correct content-disposition
resp['Content-Disposition'] = 'attachment; filename=%s' % "media.zip"
return resp
else:
return HttpResponseRedirect(reverse('report-detail', args=(pk)))
def add_comment(request, report_id):
if request.method == 'POST':
# Get the information from the post
title = request.POST.get('title')
description = request.POST.get('description')
# Get the associated report
report = Report.objects.get(id=report_id)
# Create and save a comment with the new info
comment = Comment(title=title, description=description, report=report)
comment.created_by = request.user
comment.updated_by = request.user
comment.save()
# Return to the report view
return HttpResponseRedirect(reverse('report-detail', args=(report_id)))
class CommentUpdateView(UpdateView):
model = Comment
fields = "__all__"
template_name = "comment_edit.html"
def form_valid(self, form):
form.instance.updated_by = self.request.user
return super(CommentUpdateView, self).form_valid(form)
def get_success_url(self):
return reverse('report-detail', args=(self.object.report.id,))
class CommentDeleteView(DeleteView):
model = Comment
fields = "__all__"
template_name = "comment_confirm_delete.html"
def get_success_url(self):
return reverse('report-detail', args=(self.object.report.id,))
def media_delete(request, report_id, media_id):
media_id = int(media_id)
m = Media.objects.get(id=media_id)
m.delete()
return HttpResponseRedirect(reverse('report-edit', args=(report_id,)))
# =================================================================
# JSON views/methods for standalone app
# =================================================================
@csrf_exempt
def json_login(request):
username = request.POST.get('username')
password = request.POST.get('password')
user = authenticate(username=username, password=password)
if user and user.is_active:
resp = {
'status': 'success',
'user': {
'id': user.id,
'username': user.username,
}
}
else:
resp = {
'status': 'failure',
}
return JsonResponse(resp)
def json_report_list(request, user_id):
# Get the corresponding user
user = User.objects.get(id=user_id)
# Get the associated reports
user_group_list = user.groups.all()
query = Q(private=False) | Q(created_by=user)
for g in user_group_list:
query |= Q(authorized_groups=g)
report_list = Report.objects.filter(query).distinct().order_by('short')
report_resp_list = []
for report in report_list:
# Get all the files for a report
media_list = Media.objects.filter(report__id=report.id)
file_resp = {}
for i in range(len(media_list)):
file_str = "file" + str(i)
file_resp[file_str] = media_list[i].filename
# Create response for each report
rep_resp = {
'id': report.id,
'short': report.short,
'detailed': report.detailed,
'time': report.time,
'location': report.location,
'folder': str(report.folder),
'keywords': str(report.keywords),
'private': report.private,
'authorized_groups': str(report.authorized_groups),
'file_list': file_resp,
}
# Add report json to response
report_resp_list.append(rep_resp)
response = {'report_list': report_resp_list}
return JsonResponse(response)
def json_file_download(request, user_id, media_filename):
medias = Media.objects.filter(filename=media_filename)
# No media objects with that filename found
if len(medias) == 0:
return HttpResponse("None")
else:
media = medias[0]
response = HttpResponse(media.content, content_type=media.fileType)
response['Content-Disposition'] = 'attachment; filename=' + media.filename
user = User.objects.get(id=user_id)
email_subject = 'Account Confirmation'
email_body = "Key: " + media.key + "\n" + "IV: " + media.iv
send_mail(email_subject, email_body, 'g19securewitness@gmail.com', [user.email], fail_silently=False)
return response
|
mgstigler/cs3240-s15-team19
|
secure_witness/views.py
|
Python
|
mit
| 24,658
|
[
"VisIt"
] |
3e2f99ffa3ab5b04b8a90ae045789b2097cc7620d3f7dd8492554b93f1cfdf15
|
'''
Simple metropolis sampler class
'''
import numpy as np
np.random.seed(0)
def Metropolis(n_samples, fun_calcLLK, fun_verify, data, m_ini, prior_bounds,
prop_cov):
'''
Metropolis algorithm
Args:
* n_samples: Number of samples
* fun_calcLLK: Function to calculate Log-likelihood
* fun_verify: Function to verify model
* data: Data
* m_ini: Initial model
* prior_bounds: Parameter bounds (uniform priors)
* prop_cov: Covariance of the (gaussian) proposal PDF
'''
# Initiate model chain
M = np.zeros((n_samples,m_ini.size))
LLK = np.zeros((n_samples,))
M[0,:] = m_ini # Initialize the chain
LLK[0] = fun_calcLLK(m_ini,data)
# Proposal mean
prop_mean = np.zeros(m_ini.shape)
# Iteration loop
count = 0 # Number of accepted models
for i in range(1,n_samples):
# Random walk
Mnew = M[i-1,:].copy()
Mnew += np.random.multivariate_normal(prop_mean,prop_cov)
# Check if model sample is within prior
valid = fun_verify(Mnew,prior_bounds)
if not valid:
M[i,:] = M[i-1,:].copy()
LLK[i] = LLK[i-1]
continue
# LLK of new model
logLLKn = fun_calcLLK(Mnew, data)
dLLK = logLLKn - LLK[i-1]
# Metropolis acceptance/rejection
accept = 0
U = np.log(np.random.rand())
if U < dLLK:
accept=1
else:
accept=0
# Update model
if accept:
M[i,:] = Mnew.copy()
LLK[i] = logLLKn
count += 1
else:
M[i,:] = M[i-1,:].copy()
LLK[i] = LLK[i-1]
return M,LLK,count
|
amaggi/am_bayes
|
teaching_eqloc/Metropolis.py
|
Python
|
gpl-2.0
| 1,767
|
[
"Gaussian"
] |
9619a04dd8c6192560ea0a74b41d061a9d74dd9b359f54484ac24598cbb26b4f
|
# Copyright (c) 2006-2013 Regents of the University of Minnesota.
# For licensing terms, see the file LICENSE.
import copy
import datetime
from lxml import etree
import os
import psycopg2
import sys
import time
import traceback
import uuid
import conf
import g
from grax.access_level import Access_Level
from grax.access_scope import Access_Scope
from grax.library_squelch import Library_Squelch
from grax.user import User
from gwis.query_filters import Query_Filters
from gwis.exception.gwis_error import GWIS_Error
from gwis.exception.gwis_warning import GWIS_Warning
from item import geofeature
from item import item_base
from item import item_revisionless
from item import item_user_watching
from item import item_versioned
from item.feat import byway
from item.feat import route_step
from item.feat import route_stop
from item.grac import group
from item.util import revision
from item.util.item_type import Item_Type
from item.util import ratings
from planner.travel_mode import Travel_Mode
import planner.routed_p1.route_finder
import planner.routed_p2.route_finder
import planner.routed_p3.route_finder
from util_ import geometry
from util_ import gml
from util_ import misc
from util_.log_progger import Debug_Progress_Logger
import VERSION
log = g.log.getLogger('route')
class Geofeature_Layer(object):
# SYNC_ME: Search geofeature_layer table. Search draw_class table, too.
Default = 105
# SYNC_ME: pyserver/item/feat/route.py::route.Geofeature_Layer.Z_DEFAULT
# flashclient/items/feats/Route.as::Route.z_level_always
Z_DEFAULT = 160
class One(geofeature.One):
'''A route from one byway node to another.'''
item_type_id = Item_Type.ROUTE
item_type_table = 'route'
item_gwis_abbrev = 'rt'
child_item_types = None
gfl_types = Geofeature_Layer
local_defns = [
# py/psql name, deft, send?, pkey?, pytyp, reqv, abbrev
# The user can edit 'details' to provide a description of the route.
('details', None, True, False, str, 0),
# In old CcpV1, 'from_addr' and 'to_addr' were stored in the route
# table. For Route Sharing, those columns were removed and we used the
# route_stop table to look them up. But in CcpV2 we want to cache these
# values, like we cache other origin/destination information, so it's
# quicker (and easier for devs) to get route metadata.
# RENAMED: Were: from_addr and to_addr / Now: beg_addr and fin_addr.
('beg_addr', None, True, False, str, 3,),
('fin_addr', None, True, False, str, 3,),
# BUG nnnn: The client recomputes the length, but we have it here.
# FIXME: Should this include transit edge lengths?
# The rsn_len is the length of bicycle (non-transit) route steps.
# The client can recompute this from route step lengths, which
# flashclient does when a user drags a route and flashclient
# "stitches" a sequence of routes together (though why flashclient
# doesn't just add up each sequence's rsn_lens is a mystery).
('rsn_len', None, True, None, float, 3,),
# The client can either figure these values out from the steps or we can.
('rsn_min', None, True, None, int, 3,),
('rsn_max', None, True, None, int, 3,),
('n_steps', None, True, None, int, 3,),
('beg_nid', None, True, None, int, 3,),
('fin_nid', None, True, None, int, 3,),
# BUG nnnn/MAYBE: In the client, show the avg edge weight for the route,
# and highlight byways by their edge cost for whatever algorithm was
# used. Historically, we've had a feature to color each byway by its
# rating, so maybe it would be useful to color each byway by the edge
# weight the finder used, e.g., so the user can differentiate between
# the "better" parts and the "worse" parts of the route.
# Currently, ccp.py at leasy shows you the average cost, and you can
# poke your head in the GWIS/XML to see each step's edge weight.
('avg_cost', None, True, None, float, 3,),
('stale_steps', None, True, None, int, None,),
('stale_nodes', None, True, None, int, None,),
# The travel mode indicates the planner used to generate the route.
('travel_mode', 0, True, False, int, 0,),
# When the user requests a new route, the client sends the planner
# preferences separately, in the route_get command. When the user
# modifies a route and saves a new version, the planner options are
# also meaningless, since they apply only to generating the initial
# route. However, that's not to say we can't at least send these
# values to the client on route checkout. Historically, a user looking
# at an old route wouldn't know what planner preferences were used to
# generate that route. Well, now they will. Also, by sending these
# values to the client, the client can help a user recreate a route
# request, and not just by using the same destinations, but by
# configuring the planner with the same options, too.
# p1 Planner options.
('p1_priority', None, True, None, float, 3,),
# p2 Planner options.
# [lb] renamed the two multimodal preferences because android doesn't
# use the multimodal planner, so we don't have to worry about backwards
# compatibility by preserving the old GWIS name.
('p2_depart_at', '', True, None, str, 3,),
('p2_transit_pref', 0, True, None, int, 3,),
# p3 Planner options.
('p3_weight_attr', '', True, None, str, 3,),
('p3_weight_type', '', True, None, str, 3,),
('p3_rating_pump', 0, True, None, int, 3,),
('p3_burden_pump', 0, True, None, int, 3,),
('p3_spalgorithm', '', True, None, str, 3,),
# Personalized Planner options (always-on in p1 and p2; opt-in in p3).
# Skipping/meaningless to client: rating_min.
# See __slots__ for 'tagprefs'.
# MAYBE: Send tagprefs route each route back to client?
('tags_use_defaults', False, True, None, bool, 3,),
# NOTE: We lock-down the z_level: it's neither sent to nor received from
# the client. The client figures out its own layering for routes.
# I [lb] think we only have it here to keep geofeature happy...
# MAYBE: Just consolidate byway.z and route.z in geofeature.z.
('z', None, False, None, int, 0,),
]
attr_defns = geofeature.One.attr_defns + local_defns
psql_defns = geofeature.One.psql_defns
gwis_defns = item_base.One.attr_defns_reduce_for_gwis(attr_defns)
#
private_defns = geofeature.One.psql_defns + local_defns
ctrlled_tag_sids = None
__slots__ = [
# For a calculated route, rsteps is a list of route steps (or line
# segments that determine the path of the route), and rstops is a
# list of route stops (or important points to visit along the path).
'rsteps', # In CcpV1, this was named 'path'.
'rstops',
'tagprefs',
'stale_byway_sids',
'stop_steps_stale',
'filled_path',
] + [attr_defn[0] for attr_defn in local_defns]
# *** Constructor
#
def __init__(self, qb=None, row=None, req=None, copy_from=None):
g.assurt(copy_from is None) # Not supported for this class.
#self.geofeature_layer_id = Geofeature_Layer.Default
geofeature.One.__init__(self, qb, row, req, copy_from)
# In CcpV1, steps and stops were just lists, but in CcpV2 we've made 'em
# true class objects.
self.rsteps = route_step.Many()
self.rstops = route_stop.Many()
self.tagprefs = dict()
self.filled_path = False
if row is None:
self.setup_item_revisionless_defaults(qb, force=True)
#
def __str__(self):
return ('"%s" [%s] { beg: "%s" } { end: "%s" } %s'
% (self.name,
self.__str_deets__(),
self.beg_addr,
self.fin_addr,
'[mode:%d|3attr:%s|p3wgt:%s|p3rat:%s|p3fac:%s|p3alg:%s]'
% (self.travel_mode,
self.p3_weight_attr,
self.p3_weight_type,
self.p3_rating_pump,
self.p3_burden_pump,
self.p3_spalgorithm,
),))
# *** GML/XML Processing
#
def append_gml(self, elem, need_digest):
# Call base class. We could also do, e.g.,
# route_elem = elem.findall('./route')[0]
route_elem = geofeature.One.append_gml(self, elem, need_digest)
# notify the client if the sessions match, but we don't want to
# actually send out session ids since the route may not be going to the
# original creator.
# NOTE: If the packet came locally from the route finder (for route
# analysis), the req object is not set.
log.verbose('append_gml: appending %d route steps' % (len(self.rsteps),))
for rstep in self.rsteps:
rstep.append_gml(route_elem)
log.verbose('append_gml: appending %d route stops' % (len(self.rstops),))
for rstop in self.rstops:
rstop.append_gml(route_elem)
return route_elem
#
def append_gml_geometry(self, new):
gml.append_LineString(new, self.geometry_svg)
#
def from_gml(self, qb, elem):
# The route analysis route finder ('analysis', not 'general') does not
# save routes to the database, so the stack ID isn't set.
if elem.get('stid') is None:
elem.set('stid', '0')
# MAYBE: Will stack_id=0 cause problems later?
# See item_versioned.from_gml.
# (But so far, [lb] hasn't noticed any issues... but he hasn't
# spent much time testing the route analysis tool recently).
# Now call the base class (after making sure 'stid' is set).
geofeature.One.from_gml(self, qb, elem)
self.setup_item_revisionless_defaults(qb, force=True)
# Loading rsteps and rstops is optional so that we can use this class
# and this fcn. to load what CcpV1 calls route_metadata, or just details
# about routes. In CcpV2, we don't want to repeat code, and we want to
# use Many() and One() for route just like we do for other item classes.
# Append the route steps to the route -- the route steps are the line
# segments that each represent one byway.
# NOTE: These should be the same: findall('./step/*'), findall('step').
# MAYBE: Does/should this search use dont_fetchall? Should it?
# MAYBE: This should be renamed 'rstep' but android still uses this name.
for step in elem.findall('step'):
rs = route_step.One()
rs.from_gml(qb, step)
self.rsteps.append(rs)
# MAYBE: Does/should this search use dont_fetchall? Should it?
# MAYBE: Use findall('./stop/*') instead of findall('stop')?
# Does it matter?
# MAYBE: This should be renamed 'rstop' but android still uses this name.
for stop in elem.findall('waypoint'):
rw = route_stop.One()
rw.from_gml(qb, stop)
self.rstops.append(rw)
if (not self.rsteps) or (not self.rstops):
log.error('from_gml: no steps and/or stops: %d and/or %d'
% (len(self.rsteps), len(self.rstops),))
# FIXME: This fcn. isn't called for style changes, is it?
# If not, we should raise an error.
# We'll find out if logcheck reports any of these errors...
# MAYBE?: raise GWIS_Error('Missing steps or stops for route.')
# ***
#
def as_gpx(self, db):
# Bug 1126: lxml Python warnings in error.log.
# as_gpx() sets 'xmlns:xsi=asdf'
# and 'xsi:schemaLocation=asdf'
# When loading apache, it writes to
# /var/log/apache2/error.log:
# TagNameWarning: Tag names must not contain ':',
# lxml 2.0 will enforce well-formed tag names as
# required by the XML specification.
# From: http://stackoverflow.com/questions/3685374/
# how-to-set-a-namespace-prefix-in-an-attribute-value-using-the-lxml
# See also: http://lxml.de/tutorial.html#namespaces
# Oh, wait, see also: http://stackoverflow.com/questions/8432912/
# lxml-tag-name-with-a
# 2012.09.29: Adding nsmap and replacing colons with {}s.
xsi = 'http://www.w3.org/2001/XMLSchema-instance'
xmlns = 'http://www.topografix.com/GPX/1/1'
schemaLocation = ('%s %s'
% ('http://www.topografix.com/GPX/1/1',
'http://www.topografix.com/GPX/1/1/gpx.xsd',))
version = '1.1'
# Define the namespace map.
# Wrong: schema_nsmap = {'xmlns':'xmlns', 'xsi':'xsi',}
# This adds two attr-value pairs to the XML:
# <gpx xmlns:xmlns="xmlns" xmlns:xsi="xsi" ... />
# Do this instead, per http://stackoverflow.com/questions/2850823/
# multiple-xml-namespaces-in-tag-with-lxml
schema_nsmap = {'xsi': xsi, None: xmlns,}
gpx = etree.Element(
'{%s}gpx' % (xmlns,),
version=version,
creator='Cyclopath - http://cyclopath.org',
# lxml will remove the braces and replace with a trailing colon.
attrib={'{%s}schemaLocation' % (xsi,): schemaLocation},
nsmap=schema_nsmap)
# build up the metadata element
meta = etree.SubElement(gpx, 'metadata')
author = etree.SubElement(meta, 'author')
name = etree.SubElement(author, 'name')
name.text = 'Cyclopath'
email = etree.SubElement(author, 'email')
misc.xa_set(email, 'id', 'info')
misc.xa_set(email, 'domain', 'cyclopath.org')
link = etree.SubElement(author, 'link')
misc.xa_set(link, 'href', 'http://cyclopath.org')
route = etree.SubElement(gpx, 'trk')
comment = etree.SubElement(route, 'cmt')
# 2012.09.26: FIXME: I'm not sure if we've set beg_addr and fin_addr...
# but it feels like we should have.
g.assurt(self.beg_addr == self.rstops[0].name)
g.assurt(self.fin_addr == self.rstops[-1].name)
beg_name = self.rstops[0].name
if beg_name is None:
beg_name = 'Point entered in map'
fin_name = self.rstops[-1].name
if fin_name is None:
fin_name = 'Point entered in map'
comment.text = beg_name + ' to ' + fin_name
desc = etree.SubElement(route, 'desc')
desc.text = 'Cyclopath route from ' + comment.text
# FIXME: Why are route steps being append to 'trkseg', which sounds like
# something for tracks? Why 'trk'? Because GPX?
track = etree.SubElement(route, 'trkseg')
#
# QUESTION: Does for i in xrange(len(y)) produce the
# same-ordered list as for x in y?
# I.e., why can't we for step in rsteps?
# The code in CcpV1 seems weird since rsteps is already an ordered
# sequence, but it xranged the list to send the route step its step
# number.
# CcpV1: for i in xrange(len(self.rsteps))
# But I think it may have been copied from save_core, where we use xrange
# since the route steps have been assigned step_numbers yet.
for step in self.rsteps:
step.append_gpx(db, track, self)
return gpx
#
def as_xml(self, db, as_gpx, appendage=None, appage_nom=None):
if as_gpx:
doc = self.as_gpx(db)
g.assurt(not appendage)
else:
# This is a hack since routed calls this fcn. and we're not part of
# the command hier.
doc = etree.Element('data',
rid_max=str(revision.Revision.revision_max(db)),
major=VERSION.major,
gwis_version=conf.gwis_version)
self.append_gml(doc, need_digest=False)
if appendage:
g.assurt(appage_nom)
doc.find(appage_nom).append(appendage)
return etree.tostring(doc, pretty_print=as_gpx)
# FIXME: Check usages of this fcn., to make sure the returned result is
# okay. The problem is that this fcn. (or the PostGIS fcn. it uses) finds
# the line segment nearest the pt, and then finds the endpoint nearest that
# pt. This affects the route finder, esp. when routing to/from a point near
# a long line segment (the route finder will tell you to start/end at the
# end point, but it probably makes more sense to find the vertex nearest the
# point...).
# BUG nnnn: Use m-values when routing. Client sends x,y pts to and from, and
# we find the nearesy byways, so we should also find the m-value and send
# that back so the client can draw the route line more accurately.
@staticmethod
def byway_closest_xy(qb, addr_name, pt_xy, rating_func, rating_min,
is_latlon, radius=None):
'''Return the ID of the byway node nearest to pt_xy (x,y) which is on a
byway with rating greater than or equal to rating_min for user
username. On failure, raise GWIS_Error.'''
closest_byway = None
if not is_latlon:
# E.g., "ST_GeomFromEWKT('SRID=%d;POINT(%.6f %.6f)')"
point_sql = geometry.xy_to_raw_point_lossless(pt_xy)
else:
# E.g., "ST_GeomFromEWKT('SRID=%d;POINT(%.6f %.6f)')"
point_sql = geometry.xy_to_raw_point_lossless(pt_xy,
srid=conf.srid_latlon)
point_sql = "ST_Transform(%s, %d)" % (point_sql, conf.default_srid,)
if radius is None:
the_radius = conf.geocode_filter_radius # 1000
# Don't do 100: it takes a long time.
# 1000.0, 10000.0, 100000.0: 1, 10, 100 Km
#magnitudes = (1, 10, 100,)
# MAYBE: Even 10 seems way too far to look.
magnitudes = (1, 10,)
else:
the_radius = radius
magnitudes = (1,)
g.assurt(qb.viewport.include is None)
g.assurt(qb.viewport.exclude is None)
g.assurt(qb.filters == Query_Filters(None))
# FIXME: Skip this for-loop and test just slow to make sure it works.
go_slow = False
for scalar in magnitudes:
try_radius = the_radius * scalar
closest_byway = One.byway_closest_xy_find(
qb, go_slow, rating_func, rating_min, point_sql, try_radius)
if closest_byway is not None:
break
else:
log.debug('byway_closest_xy/fast: not found at radius: %s'
% (try_radius,))
if radius is None:
if closest_byway is None:
log.debug('byway_closest_xy/fast: no byway for point_sql: %s'
% (point_sql,))
go_slow = True
closest_byway = One.byway_closest_xy_find(
qb, go_slow, rating_func, rating_min, point_sql)
if closest_byway is None:
log.warning('byway_closest_xy/slow: no byway for point_sql: %s'
% (point_sql,))
raise GWIS_Error('No routable streets or trails near "%s".'
% (addr_name,))
# Reset the filters... we checked above that these weren't special.
qb.filters = Query_Filters(None)
return closest_byway
#
# FIXME: 2012.08.02: Use new node_endpoint table?
@staticmethod
def byway_closest_xy_find(qb, go_slow, rating_func, rating_min, point_sql,
radius=None):
''' ... '''
closest_byway = None
g.assurt((not go_slow and radius is not None)
or (go_slow and radius is None))
g.assurt(qb.finalized)
# FIXME: MAGIC NUMBER: Analyze loop and see if 10 should be increased.
qb.filters.pagin_count = 10
qb.filters.pagin_offset = 0
give_up = False
while not give_up:
byways = byway.Many()
byways.search_by_distance(qb, point_sql, radius)
# sets 'st_line_locate_point', an m-value
if len(byways) == 0:
give_up = True
else:
closest_byway = One.byway_closest_xy_find_nearest(qb,
byways, rating_func, rating_min)
if closest_byway is not None:
give_up = True
if not give_up:
log.info('byway_closest_xy_find: not giving up...')
qb.filters.pagin_offset += qb.filters.pagin_count
return closest_byway
#
@staticmethod
def byway_closest_xy_find_nearest(qb, byways, rating_func, rating_min):
closest_byway = None
for byway_ in byways:
# BUG 2340: Cannot always route to/from a point that gets
# associated with a one_way, so, as a temporary solution, don't
# choose the node of a one_way!
# FIXME: 2011.08.05: See Bug 2340, this is messing up route finder, e.g.,
# around humprey airport, it never chooses one_ways, but it should if you're
# traveling in that direction
# 2014.04.03: Can we just not choose a one-way for the origin?
if (((rating_func is None)
or (rating_func(byway_.stack_id) >= rating_min))
# FIXME/BUG nnnn: Allow One-ways as O and/or D of O/D pair.
and (byway_.one_way == 0)
# Expressways and expressway ramps are never rideable.
and (byway_.geofeature_layer_id
# See also:
# byway.Geofeature_Layer.controlled_access_gfids
not in (byway.Geofeature_Layer.Expressway,
# NOTE: Some MnDOT ramps are not connected to
# expressways. See: Other Ramp.
# We include ramps in routes, but not as O/D, since
# we don't know if this is a true xway ramp or not.
byway.Geofeature_Layer.Expressway_Ramp,
byway.Geofeature_Layer.Railway,
byway.Geofeature_Layer.Private_Road,))):
# The byway has no rating fcn., or it's rated above the minimum;
# the byway is not a one-way;
# and the byway has a geofeature layer ID and isn't controlled,
# or an expressway ramp.
# Now see that the byway isn't tagged impassable or controlled.
is_controlled = False
One.ensure_ctrlled_tags_loaded(qb)
if One.ctrlled_tag_sids:
where_branch = revision.Revision.branch_hier_where_clause(
qb.branch_hier,
'iv',
include_gids=False,
allow_deleted=False)
lval_sql = (
"""
SELECT lv.stack_id FROM link_value AS lv
JOIN item_versioned AS iv
USING (system_id)
WHERE lv.rhs_stack_id = %d
AND lv.lhs_stack_id IN (%s)
AND %s
""" % (byway_.stack_id,
','.join([str(x) for x in One.ctrlled_tag_sids]),
where_branch,
))
rows = qb.db.sql(lval_sql)
if len(rows) > 0:
is_controlled = True
if not is_controlled:
closest_byway = byway_
break
return closest_byway
#
@staticmethod
def ensure_ctrlled_tags_loaded(qb):
# This is kinduv a late minute hack: skip byways tagged impassable.
if One.ctrlled_tag_sids is None:
One.ctrlled_tag_sids = []
qb.item_mgr.load_cache_attachments(qb)
for tag_name in byway.Geofeature_Layer.controlled_access_tags:
the_tag = qb.item_mgr.cache_tag_lookup_by_name(tag_name)
if the_tag is None:
log.warning('ensure_ctrlled_tags_loaded: Could not find tag: %s'
% (tag_name,))
else:
One.ctrlled_tag_sids.append(the_tag.stack_id)
# *** Saving to the Database
# FIXME: We need to add a row to route_step_count...
# Or maybe we can drop route_step_count and just add the column,
# step_count, to the route table?
#
def save_core(self, qb):
log.debug('save_core: route: %s / no. rsteps: %s / no. rstops: %s'
% (self, len(self.rsteps), len(self.rstops),))
g.assurt(self.stack_id > 0)
# FIXME: In CcpV1, we always make the stealth_secret/deep_link
# for public and shared routes. In CcpV2, we don't always.
# Make sure things still work well...
# We could wait for the user to ask for a so-called "deep-link", or we
# could just always make the new so-called "stealth secret". Realize that
# the presense of the stealth secret doesn't mean it's usable: the route
# still needs a GIA record for the public with a stealth access level.
# For that reason, we wait to make the stealth secret until the user
# wants it.
# Save to the base class tables.
geofeature.One.save_core(self, qb)
# Save to the route table.
self.save_insert(qb, One.item_type_table, One.private_defns)
# FIXME: What if user is just changing a route's name or details, i.e.,
# not changing any route stops. Do we still save a new version of the
# route with new copies of the same rsteps and rstops? Seems like a waste
# of space for editing metadata...
# 2014.09.08: Verified: Bug nnnn/MAYBE: Changing just the route name
# causes all the route steps to be saved again... except we're just
# taking what the client sent us and not double-checking stack IDs!
#
# FIXME: Make a route_metadata table to store name, details, etc? And
# then only change route.version and save a new route when rsteps or
# rstops changes?
# NOTE: Not doing (for step in self.rsteps) because step_numbering may
# have changed (2012.09.27: I [lb] think; I'm just guessing).
for i in xrange(len(self.rsteps)):
self.rsteps[i].save_rstep(qb, self, i)
for i in xrange(len(self.rstops)):
self.rstops[i].save_rstop(qb, self, i)
# Only save route parameters and tag preferences the first time.
if self.version == 1:
qb.db.insert(table='route_parameters',
id_cols={
'route_stack_id': self.stack_id,
'branch_id': self.branch_id,},
nonid_cols={
'travel_mode': self.travel_mode,
'p1_priority': self.p1_priority,
'p2_depart_at': self.p2_depart_at,
'p2_transit_pref': self.p2_transit_pref,
'p3_weight_attr': self.p3_weight_attr,
'p3_weight_type': self.p3_weight_type,
'p3_rating_pump': self.p3_rating_pump,
'p3_burden_pump': self.p3_burden_pump,
'p3_spalgorithm': self.p3_spalgorithm,
'tags_use_defaults': self.tags_use_defaults,
},
skip_empties=True)
for t in self.tagprefs:
qb.db.insert('route_tag_preference',
{'route_stack_id': self.stack_id,
'branch_id': self.branch_id,
'tag_stack_id': t,},
{'tpt_id': self.tagprefs[t],})
# MAYBE: This belongs in save_related_maybe. Maybe some of the previous
# code, too...
# Record a route view if this is a new, user-requested route.
if ((self.client_id < 0)
and (self.fresh)
and (qb.username != conf.anonymous_username)):
# NOTE: Not locking since we're insert_clobbering a row in route_view
# and already have the primary keys (route_id and username)...
# FIXME: Isn't there already a lock on 'revision', anyway?
g.assurt(self.version == 1)
## NO: qb.db.lock_table('route_view', 'EXCLUSIVE')
# NO: qb.db.lock_table('route_view', 'SHARE ROW EXCLUSIVE')
qb.db.insert_clobber(
'item_findability',
{'username': qb.username,
'item_stack_id': self.stack_id,},
{'user_id': qb.user_id,
# New routes are hidden by default; the user 'saves' the route
# if they want it in their library, or to edit its permissions.
'library_squelch': Library_Squelch.squelch_always_hide,
'show_in_history': True,
# Trigger will set: last_viewed.
'branch_id': self.branch_id,})
# ***
#
def save_init_item_findability(self, qb, username, user_id):
# This probably belongs in a base or utility class. But route is the only
# class to do this so far... well, see also similar code in route_get.py.
sql_exists_itm_fbily = (
"""
SELECT *
FROM item_findability
WHERE item_stack_id = %d
AND username = %s
AND branch_id = %d
""" % (self.stack_id,
qb.db.quoted(username),
qb.branch_hier[0][0],))
rows = qb.db.sql(sql_exists_itm_fbily)
if not rows:
sql_update_itm_fbily = (
"""
INSERT INTO item_findability
(item_stack_id,
username,
user_id,
library_squelch,
show_in_history,
branch_id)
VALUES
(%d, %s, %d, %d, %s, %d)
""" % (self.stack_id,
qb.db.quoted(username),
user_id,
Library_Squelch.squelch_always_hide,
'FALSE', # show_in_history,
qb.branch_hier[0][0],))
qb.db.sql(sql_update_itm_fbily)
#
def save_related_maybe(self, qb, rid):
geofeature.One.save_related_maybe(self, qb, rid)
# Update the node columns. This just has to come after save_rstep (which
# happens in save_core). Oh, and we need a system_id.
g.assurt(self.system_id > 0)
# FIXME: If we're just changing GIA permissions (not recomputing the
# route) we should skip the stats update (which recalculates the
# beg_addr, fin_addr, route_len, route_step geometry, etc).
sole_row = Many.update_node_stats(qb, system_id=self.system_id)
if sole_row:
self.beg_addr = sole_row['beg_addr']
self.fin_addr = sole_row['fin_addr']
if sole_row['lhs_forward']:
self.beg_nid = sole_row['lhs_beg_node_id']
else:
self.beg_nid = sole_row['lhs_fin_node_id']
# MAYBE/EXPLAIN: Is the final node ID the first or last node
# of the last route step byway?
if sole_row['rhs_forward']:
self.fin_nid = sole_row['rhs_fin_node_id']
else:
self.fin_nid = sole_row['rhs_beg_node_id']
self.rsn_min = sole_row['step_count_min']
self.rsn_max = sole_row['step_count_max']
self.n_steps = sole_row['step_count_count']
self.rsn_len = round(sole_row['steps_total_len'], 1)
else:
g.assurt_soft(False)
# Checkout the missing columns that just got writ and update some attrs.
self.savex_fetch_calculated_node_stats(qb)
# Save item_findability records so the route is not shown in the library.
self.save_init_item_findability(qb, conf.anonymous_username,
User.user_id_from_username(qb.db,
conf.anonymous_username))
# See save_core for what's essentially the following:
# if qb.username != conf.anonymous_username:
# self.save_init_item_findability(qb, qb.username, qb.user_id)
#
def savex_fetch_calculated_node_stats(self, qb):
# SYNC_ME: See Many.update_node_stats_process.
#
# Ignoring: beg_addr, fin_addr,
# rsn_min, rsn_max, n_steps,
# beg_nid, fin_nid
#
# MAYBE: See update_node_stats; we shouldn't need to do this:
fetch_sql = ("SELECT rsn_len FROM route WHERE system_id = %d"
% (self.system_id,))
rows = qb.db.sql(fetch_sql)
if len(rows) == 1:
row = rows[0]
if (self.rsn_len) and ((self.rsn_len - row['rsn_len']) > 1.0):
# The static update_node_stats fcn. computes route stats,
# and in save_related_maybe we apply those values to the
# route object, so what we just found in the database should
# be what we just wrote to the database. Or close enough.
log.warning('fetch_calcd_nd_stats: unexpected: rsn_len: %s / %s'
% (self.rsn_len, row['rsn_len'],))
self.rsn_len = row['rsn_len']
else:
log.error('fetch_calcd_nd_stats: nothing found sys_id: %d / rows: %d'
% (self.system_id, len(rows),))
if self.avg_cost is None:
self.avg_cost = float('inf')
# If we load the route from memory, we'll call self.fill_path, but
# if the route is from a client, it contains lightweight route
# steps, i.e., just the byway stack ID, and not rating or geometry.
# We could call byway.Many to load all the byways in the route, and
# to grab the ratings and geometries from there, but the client
# doesn't look for rsn_len or avg_cost in the commit response, so
# we're fine skipping this calculation if not filled_path.
if self.rsn_len and self.filled_path:
cumulative_cost = 0.0
for step in self.rsteps:
step.calc_length_and_cost()
try:
cumulative_cost += step.edge_weight
except TypeError:
# NOTE: The step.rating is the generic rating...
# so if the cost is the length, this is the
# wrong value...
cumulative_cost += step.rating * step.edge_length
self.avg_cost = (
(cumulative_cost / route_step.One.weight_multiplier)
/ self.rsn_len)
log.debug('fetch_calcd_nd_stats: avg_cost: %s' % (self.avg_cost,))
# end: if self.rsn_len
# end: if self.avg_cost is None
#
def setup_item_revisionless_defaults(self, qb, force=False):
geofeature.One.setup_item_revisionless_defaults(self, qb, force=True)
#
def validize_geom(self, qb, is_new_item, ref_item):
# Currently, routes themselves are geometry-less. Even though they
# derived from geofeature.
# NO: geofeature.One.validize_geom(self, qb, is_new_item, ref_item)
pass
#
def version_finalize_and_increment(self, qb, rid, same_version=False,
same_revision=False):
geofeature.One.version_finalize_and_increment(self, qb, rid,
same_version,
same_revision)
# *** Other methods
#
def fill_tagprefs(self, qb):
# Older android will continue to send Travel_Mode.bicycle, but for newer,
# non-personalized p3, we can ignore tag preferences.
if ((self.travel_mode in (Travel_Mode.bicycle,
Travel_Mode.classic,))
or ((self.travel_mode == Travel_Mode.wayward)
# MAGIC_NUMBER: 'p' as in 'prat', 'pfac', 'rac'.
and (self.p3_weight_type.startswith('p')))):
prefs = qb.db.sql(
"""
SELECT
tag_stack_id,
tpt_id
FROM
route_tag_preference
WHERE
route_stack_id = %d
AND branch_id = %d
""" % (self.stack_id,
self.branch_id,))
for row in prefs:
self.tagprefs[row['tag_stack_id']] = int(row['tpt_id'])
#
def fill_path(self, qb):
#
# Before running this function, it is is mandatory to run fill_tagprefs()
#
# compute bonus and penalty tag sets now, we'll need them to
# compute the bonus/penalty flags and modified ratings for
# rating steps (loaded below)
bonus_tags = set([t for t in self.tagprefs
if self.tagprefs[t] == ratings.t_bonus])
penal_tags = set([t for t in self.tagprefs
if self.tagprefs[t] == ratings.t_penalty])
log.debug('fill_path: bonus_tags: %s / penal_tags: %s'
% (bonus_tags, penal_tags,))
# Rating sql
rating_sql = self.prepare_rating_sql(qb)
# Route steps
# MAYBE: Move this code to route_step.
# read in all route steps, including geometry and elevation
# tag preferences and ratings will be read in per-step below
# BUG NNNN: (probably CcpV1, too): Byway Rating missing from
# routes loaded from route library.
# BUG nnnn: loading routes is slow -- ratings loaded one by one.
# NOTE: Left-outer-joining geofeature et al. so that we don't exclude
# transit steps.
rsteps_sql = (
"""
SELECT
DISTINCT ON (rs.route_id, rs.step_number)
rs.route_id,
rs.step_number,
rs.route_stack_id,
rs.route_version,
rs.byway_id,
rs.byway_stack_id,
rs.byway_version,
--iv.valid_until_rid AS byway_until_rid,
COALESCE(rs.step_name, iv.name) AS step_name,
rs.beg_time,
rs.fin_time,
rs.travel_mode,
length2d(gf.geometry) AS length,
rs.forward,
gf.geofeature_layer_id AS byway_geofeature_layer_id,
gf.beg_node_id,
gf.fin_node_id,
gf_latest.beg_node_id AS latest_beg_node_id,
gf_latest.fin_node_id AS latest_fin_node_id,
--gf.one_way AS byway_one_way,
gf_latest.beg_node_id AS latest_one_way,
CASE
WHEN transit_geometry is null
THEN ST_AsSVG(ST_Scale(gf.geometry, 1, -1, 1), 0, %d)
ELSE ST_AsSVG(ST_Scale(transit_geometry, 1, -1, 1), 0, %d)
END AS geometry,
-- These are not used:
nel_iv.name AS node_lhs_name,
ner_iv.name AS node_rhs_name
FROM route_step AS rs
LEFT OUTER JOIN geofeature AS gf
ON (gf.system_id = rs.byway_id)
LEFT OUTER JOIN item_versioned AS iv
ON (iv.system_id = gf.system_id)
LEFT OUTER JOIN geofeature AS gf_latest
ON (gf_latest.stack_id = rs.byway_stack_id)
LEFT OUTER JOIN item_versioned AS iv_latest
ON (iv_latest.system_id = gf_latest.system_id)
LEFT OUTER JOIN node_endpoint AS nel
ON (nel.stack_id = gf.beg_node_id)
LEFT OUTER JOIN item_versioned AS nel_iv
ON (nel_iv.system_id = nel.system_id)
LEFT OUTER JOIN node_endpoint AS ner
ON (ner.stack_id = gf.fin_node_id)
LEFT OUTER JOIN item_versioned AS ner_iv
ON (ner_iv.system_id = ner.system_id)
WHERE
rs.route_id = %d
-- MAYBE: Only supporting latest elevation data, i.e., not historic
AND nel_iv.valid_until_rid = %d
AND ner_iv.valid_until_rid = %d
AND iv_latest.valid_until_rid = %d
ORDER BY
rs.step_number ASC
""" % (conf.db_fetch_precision,
conf.db_fetch_precision,
self.system_id,
conf.rid_inf,
conf.rid_inf,
conf.rid_inf,
))
time_0 = time.time()
rstep_rows = qb.db.sql(rsteps_sql)
log.debug('fill_path: found %d route steps in %s'
% (len(rstep_rows), misc.time_format_elapsed(time_0),))
time_0 = time.time()
self.stale_nodes = 0
self.stale_byway_sids = []
self.stop_steps_stale = {}
#self.stale_steps = 0
# Primer. So that we have all stop numbers ready to iterate.
for stop_num in xrange(len(self.rstops)):
self.stop_steps_stale[stop_num] = []
curr_stop_num = 0
last_stop_num = len(self.rstops) - 1
next_stop = None
last_rstep = None
rstep_num = 0
gap_hack = None
for row in rstep_rows:
step = route_step.One(qb, row=row)
if last_rstep is not None:
# 2013.04.29: Query above was not DISTINCTing, so we were seeing
# contiguous route steps for the same byway segment.
g.assurt(last_rstep != step)
else:
# E.g., self.rstops[0].stop_step_number = 0
self.rstops[curr_stop_num].stop_step_number = rstep_num
if step.byway_stack_id is not None:
# MAYBE: It's up to the client to send all these values.
# Should we verify them? Or maybe just fetch the
# system_id so the client doesn't have to send it?
g.assurt(step.byway_id > 0)
g.assurt(step.byway_stack_id > 0)
g.assurt(step.byway_version > 0)
if last_rstep is None:
# This happens only the first time through the for loop.
warn_nid = False
if step.forward:
if self.rstops[0].node_id != step.beg_node_id:
warn_nid = True
else:
if self.rstops[0].node_id != step.fin_node_id:
warn_nid = True
if warn_nid:
# This might happen if the user drags an endpoint
# destination, since the node ID will be unique and not match
# a road? Or do we always snap to the closest byway node?
log.warning(
'fill_path: rstops[0].nid != step[0].nid: %s / %s'
% (self.rstops[0], step,))
self.rstops[curr_stop_num].stop_step_number = rstep_num # 0
next_stop = self.rstops[curr_stop_num+1] # I.e., [1]
# We could compare byway_one_way != latest_one_way
# but checking latest_one_way vs. step.forward seems
# more properer.
if ( (step.beg_node_id != step.latest_beg_node_id)
or (step.fin_node_id != step.latest_fin_node_id)
or ((step.latest_one_way == 1) and (not step.forward))
or ((step.latest_one_way == -1) and (step.forward))):
self.stale_nodes += 1
# We really only need this list when route is fetched w/
# check_invalid.
self.stale_byway_sids.append(step.byway_stack_id)
misc.dict_list_append(self.stop_steps_stale,
curr_stop_num,
step.byway_stack_id)
#if step.byway_until_rid < conf.rid_inf:
# self.stale_steps += 1
# Check if this edge starts from a route stop. This applies to
# all route stops except the last, 'natch.
if (rstep_num > 0) and (curr_stop_num < last_stop_num):
found_next_stop = False
if next_stop.node_id == step.beg_node_id:
if step.forward:
found_next_stop = True
gap_hack = None
else:
# This should be the route step leading into the stop,
# and the next step is the one we want, leading away.
# Unless this is one of the buggy routes...
gap_hack = step
elif next_stop.node_id == step.fin_node_id:
if not step.forward:
found_next_stop = True
gap_hack = None
else:
# This should be the route step leading into the stop.
gap_hack = step
elif gap_hack is not None:
# This step does not share a node with the last
# step, and the last step was a stop... oy.
log.warning('fill_path: gap_hack: step: %s / %s'
% (str(step), self,))
curr_stop_num += 1
self.rstops[curr_stop_num].stop_step_number = rstep_num - 1
next_stop = self.rstops[curr_stop_num+1]
gap_hack = None
elif next_stop.node_id == 0:
# FIXME/BUG nnnn: Fix routes in db with missing node IDs
# ccpv3_live=> select * from _rt_stop where rt_stk_id = 4120056;
# rt_v | stop | rs_nom | x | y | nd_id |
# ------+------+------------------+-----------+------------+---------+
# 1 | 0 | Gateway Fountain | 478882.96 | 4981091 | 1301266 |
# 1 | 1 | Edina, MN | 472560.76 | 4973173.34 | 1239800 |
# 2 | 0 | Gateway Fountain | 478882.96 | 4981091 | 1301266 |
# 2 | 1 | | 474846.40 | 4975076.5 | 0 |
# 2 | 2 | Edina, MN | 472560.76 | 4973173.34 | 1239800 |
pass
if found_next_stop:
curr_stop_num += 1
self.rstops[curr_stop_num].stop_step_number = rstep_num
next_stop = self.rstops[curr_stop_num+1]
# Query to get rating (user's or generic rater's).
#
# MAYBE: Do one bulk SQL for ratings rather than loading them each
# individually. E.g., move this sql() outside of the for
# loop and run it just once... [lb] usually sees fetching
# all the rows one of the time as being faster than fetching
# one of the rows all of the time (i.e., for any SQL query,
# and not just for ratings).
# BUG nnnn/INVESTIGATE: Try a long route without getting personal
# ratings and see if checking out existing
# routes is any faster. If so, rework this
# sql so we get all ratings in one SQL query.
#
rating_rows = qb.db.sql(rating_sql % (step.byway_stack_id,))
if len(rating_rows) > 0:
rating = rating_rows[0]['value']
else:
rating = None
if bonus_tags or penal_tags:
# query to get tag applications on route-step's byway segment
# FIXME: this query is similar to tag query in ratings.py.
# FIXME: This ignores permissions.
# FIXME: Maybe we should get all the byway stack IDs for all the
# route steps and bulk-load the byways with tags populated?
tag_rows = qb.db.sql(
"""
SELECT
lv.lhs_stack_id AS tag_id
FROM
link_value AS lv
JOIN group_item_access AS gia
ON (gia.item_id = lv.system_id
AND gia.item_type_id = %d)
WHERE
lv.branch_id = %d
AND gia.valid_until_rid = %d
AND gia.link_lhs_type_id = %d
AND gia.link_rhs_type_id = %d
AND NOT gia.deleted
AND lv.rhs_stack_id = %d
""" % (Item_Type.LINK_VALUE,
self.branch_id,
conf.rid_inf,
Item_Type.TAG,
Item_Type.BYWAY,
step.byway_stack_id,))
block_tags = set([int(t['tag_id']) for t in tag_rows])
bonus_ct = len(bonus_tags & block_tags)
penal_ct = len(penal_tags & block_tags)
else:
bonus_ct = 0
penal_ct = 0
# Update step based on tagging/rating information.
if rating is not None:
step.rating = ((rating + bonus_ct * 5.0 + penal_ct * 0.5)
/ (1 + bonus_ct + penal_ct))
else:
# EXPLAIN: This path ignored in CcpV1. Why?
# See, e.g.: 1416896 (W Bush Lake Rd).
# Where's its generic rating?
# It's just got three user ratings...
# and it's deleted!
# Ideally, we'd log a warning if not byway.deleted,
# but we don't have a handle on the byway, and it's
# not important enough to add more SQL.
log.debug('fill_path: no generic rating: byway prob deleted: %s'
% (str(step),))
step.bonus_tagged = (bonus_ct > 0);
step.penalty_tagged = (penal_ct > 0);
else:
# This is a transit step that isn't tied to a rateable byway.
step.rating = 3.0
step.bonus_tagged = 0.0
step.penalty_tagged = 0.0
self.rsteps.append(step)
rstep_num += 1
last_rstep = step
# end: for row in rstep_rows
self.rstops[-1].stop_step_number = rstep_num - 1
# There's at least one route, e.g., Stk ID 1582594,
# that has a route stop whose node ID only matches one of the
# route steps (in the example route, named "molly quinn to Humphry"
# the edge leading into the stop shares a node ID, but not the
# escape edge. I [lb] also see that version=2 of the route steps
# have no names in the database, so it looks like there were some
# issues when the route was last saved.
rstop_i = 0
while rstop_i < len(self.rstops):
try:
self.rstops[rstop_i].stop_step_number
# Success!
except AttributeError:
log.warning('did not find route step for route stop: %d / %s'
% (rstop_i, self,))
if rstop_i <= 0:
step_num = 0
elif rstop_i >= (len(self.rstops) - 1):
step_num = len(self.rsteps)
else:
step_num = self.rstops[rstop_i-1].stop_step_number
self.rstops[rstop_i].stop_step_number = step_num
rstop_i += 1
if (curr_stop_num + 1) != last_stop_num:
log.warning(
'fill_path: curr_stop_num + 1 != last_stop_num: %d + 1 != %d'
% (curr_stop_num, last_stop_num,))
log.debug('fill_path: processed %d route steps in %s'
% (len(rstep_rows), misc.time_format_elapsed(time_0),))
log.debug('fill_path: stale_nodes: %d' % (self.stale_nodes,))
self.filled_path = True
#
def prepare_rating_sql(self, qb):
# Create a sql string that will load a user's rating on a byway,
# Or the generic rating if there is no user or the user hasnt rated it
if qb.username == conf.anonymous_username:
rating_sql = (
"""
SELECT
value
FROM
byway_rating
WHERE
username = '%s'
AND byway_stack_id = %%d
AND branch_id = %d
""" % (conf.generic_rater_username,
self.branch_id,))
else:
rating_sql = (
"""
SELECT
CASE WHEN r2.value IS NULL
THEN r1.value
ELSE r2.value
END AS value
FROM
byway_rating AS r1
LEFT JOIN
byway_rating AS r2
ON (r2.byway_stack_id = r1.byway_stack_id
AND r2.branch_id = r1.branch_id
AND r2.username=%s)
WHERE
r1.username = '%s'
AND r1.byway_stack_id = %%d
AND r1.branch_id = %d
""" % (qb.db.quoted(qb.username),
conf.generic_rater_username,
self.branch_id))
return rating_sql
# ***
#
def steps_fill_geometry(self, qb):
# NOTE: This uses the route's path to construct the geometry. It does
# not assume that the route is actually one that is saved in the
# database.
# Currently it's just used by route analysis to make WKT for
# the Shapefile.
byway_ids = list()
for rstep in self.rsteps:
byway_ids.append(rstep.byway_id)
res = qb.db.sql(
"""
SELECT
ST_AsText(ST_Collect(gf.geometry)) AS geometry_wkt
FROM
geofeature AS gf
WHERE
gf.system_id IN (%s)
""" % (", ".join(map(str, byway_ids)),))
g.assurt(len(res) == 1)
self.set_geometry_wkt(res[0]['geometry_wkt'], is_changed=True)
#
# Similar To (S.t.) item_user_access.prepare_and_save_item
def prepare_and_commit_revisionless(self, qb, grac_mgr):
log.debug('prepare_and_commit_revisionless: saving route to database')
# MAYBE: Use the geometry field? We at least have to make it
# POLYGON EMPTY or LINESTRING EMPTY (they're both the same value,
# so it doesn't matter: 01070000202369000000000000 (if you use
# ST_AsText you'll get GEOMETRYCOLLECTION EMPTY)).
# No: self.set_geometry_wkt(geometry_wkt=None, is_changed=None)
if not self.geometry_wkt:
self.geometry_wkt = 'LINESTRING EMPTY'
else:
log.warning('prep_n_commit_rvsnlss: Unexpected: geometry_wkt?: %s'
% (str(self),))
# Since we're using an existing revision ID and using the sequences to
# get new stack IDs and system IDs, we don't need to lock any tables,
# and we don't need to worry about duplicate IDs since we just got new
# ones from the sequences. So start a r/w session but don't bother
# locking any tables.
qb.db.transaction_begin_rw()
# NOTE: Trample grac_mgr and ignore item_mgr. This has to come after
# starting the rw transaction, since prepare_mgr gets row locks on NIP.
qb.grac_mgr = grac_mgr
qb.grac_mgr.prepare_mgr('user', qb)
# In old CcpV1 (before route sharing), valid_start_rid existed but wasn't
# used (it was added in schema script 058; though the table had a
# last_modified column since 008 until it got recreated as the created
# column in 067, and last_modified wasn't dropped until 079, and then
# created was booted in 246, replaced by item_revisionless.edited_date).
# So the V1->V2 SQL update just tags all the routes without revisions as
# being revisioned at the revision of the upgrade. This should be fine,
# since we also don't have access records for the old routes (so old
# routes are just used for research purposes only, while new routes can
# be added to a user's route library, etc.).
#
# Also in old CcpV1, all saved route changes are revisioned. Which floods
# the revision history with "auto-updated" revisions (whenever someone
# opens a route whose streets have been edited, the route is updated and
# auto-saved, and the revision history reflects this).
#
# In CcpV2, [lb] argues that the revision history should be for
# meaningful map edits, and not for routes. The only drawback is that
# you cannot revert route edits, but the CcpV1 behavious is so buggy!
#
# BUG nnnn/CcpV1: Whenever you load a route, it rechecks road geometry.
# Even if you don't save 'Use Suggested Fix', the route
# is saved with a new revision. If you refresh
# flashclient and reopen the map, the same thing happens!
# That is, another revision is created and the route is
# saved again! This is probably because the route fetch
# is thinking the route was last updated and the current
# revision minus one, even though the new revision was
# only because of route changes! In other words, the
# route finder thinks that all revision changes
# necessitate rechecking routes, even though, in CcpV1
# since route sharing was added, most revisions are just
# routes been auto-updated. Oy!
#
# Bug nnnn/CcpV1: Like I said above, if you don't revision routes, you
# cannot revert them, but in CcpV1, you cannot tell what
# route you're reverting, anyway! If you
#
# Bug nnnn/CcpV1: It seems like loading a route from the library always
# takes a while becuase the route is being recomputed.
# Another forehead-slapper! We should load the route
# first, and then flashclient should ask the server --
# in the background, so the user can start working with
# the route -- if anything changed, and then flashclient
# can reveal a widget if an updated route is returned.
#
qb.item_mgr.start_new_revision(qb.db, use_latest_rid=True)
log.debug('prep_n_commit_rvsnlss: using latest rev for new rt: rev ID %d'
% (qb.item_mgr.rid_new,))
# To set the stack ID, if we were making a new revision, we'd use
# negative client IDs, e.g.,
# self.stack_id = -1
# self.stack_id_correct(qb)
# But we're not making a new revision, so we can just pluck the next
# stack ID value directly from the sequence.
if self.stack_id < 0:
client_id = self.stack_id
if (self.stack_id is None) or (self.stack_id < 0):
self.stack_id = qb.item_mgr.seq_id_steal_stack_id(qb.db)
g.assurt(self.version == 0)
self.fresh = True
else:
# Otherwise, keep the same stack ID. We'll also keep the same version.
g.assurt(self.version > 0)
pass
g.assurt(self.stack_id > 0)
log.debug('prep_n_commit_rvsnlss: clearing item_cache')
qb.item_mgr.item_cache_reset()
qb.item_mgr.item_cache_add(self, client_id)
# See init_permissions_new: this sets arbiter for either the session
# group or the user's private group, depending.
# The default behavior gives the user arbiter access to the route, so
# it'll show up in route search and route library. Users use
# route_view.active to remove a route from their library and search
# results.
#
# FIXME: Option to include inactive route in searches. Also make sure
# searches and the library are filtered by inactive. And maybe
# rename active to something more unique.
# FIXME: route_view.active should be True for this route. Is it?
# FIXME: See notes in scripts/schema/201-apb-60-groups-pvt_ins3.sql
# Should we add access for the basemap owners group?
# Or make a new group, called, route-spy?
prepared = qb.grac_mgr.prepare_item(qb,
self, Access_Level.editor, ref_item=None)
g.assurt(prepared)
# Save a newly requested route.
# MAYBE: Does this handle an updated, existing route?
g.assurt(self.version == 0)
self.version_finalize_and_increment(qb, qb.item_mgr.rid_new,
same_version=False)
g.assurt(self.version == 1)
self.save(qb, qb.item_mgr.rid_new)
try:
# BUG 2688: Use transaction_retryable?
qb.db.transaction_commit()
except psycopg2.IntegrityError, e:
# This can happen if a user edits a byway in the live database,
# and then we use a Shapefile from that database to start the
# route finder, and our test database is older than the edit.
advice = 'If testing, update to latest live snapshot.'
log.error('prep_n_commit_rvsnlss: %s (%s)'
% (str(e), advice,))
raise
log.debug('prep_n_commit_rvsnlss: save completed')
# ***
#
def compute_stats_raw(self):
'''
Called to compute some stats about the route, if update_node_stats
not being called because this is a transient route and not being
saved to the database. The update_node_stats fcn. calculates stats
using SQL; we have to do it using Python maths.
'''
# See: Many.node_bulk_update. We populate the same columns it does.
# Skipping: self.system_id, since this route isn't saved.
# Skipping: self.beg_addr and self.fin_addr, since they're already set.
step_count_min = sys.maxint #float('inf')
step_count_max = -sys.maxint #float('-inf')
step_count_count = 0
steps_total_len = 0.0
cumulative_cost = 0.0
for step in self.rsteps:
step_count_min = min(step_count_min, step.step_number)
step_count_max = max(step_count_max, step.step_number)
step_count_count += 1
step.calc_length_and_cost()
steps_total_len += step.edge_length
cumulative_cost += step.edge_weight
self.rsn_min = step_count_min
self.rsn_max = step_count_max
self.n_steps = step_count_count
self.rsn_len = steps_total_len
if self.avg_cost is None:
if self.rsn_len:
self.avg_cost = (
(cumulative_cost / route_step.One.weight_multiplier)
/ float(self.rsn_len))
log.debug('compute_stats_raw: avg_cost: %s' % (self.avg_cost,))
else:
self.avg_cost = float('inf')
if self.rsteps[0].forward:
self.beg_nid = self.rsteps[0].beg_node_id
else:
self.beg_nid = self.rsteps[0].fin_node_id
if self.rsteps[-1].forward:
self.fin_nid = self.rsteps[-1].beg_node_id
else:
self.fin_nid = self.rsteps[-1].fin_node_id
# ***
#
def get_friendly_name(self):
'''Compute the newly-requested route's friendly (default) name.'''
# NOTE: This fcn. runs in the context of the route finder because it
# requires that route_step.edge_length be set. The edge_length is
# only set by the route finder. Don't call this fcn from apache-pyserver.
# In old CcpV1, before route sharing, new routes were assigned a name and
# a (long) timestamp.
# 'New Route %s' % (time.strftime('%I:%M %m-%d-%y',
# time.localtime(time.time())),),
# MAYBE: This algorithm is pretty cool -- it finds the edge name
# travelled the longest and uses that for the new route name. But maybe
# we want to include the beg_stop or fin_stop, or maybe the date? Or do
# those belong as metadata, i.e., so the client can display those
# independently (e.g., the date could be in smaller font, or the user
# could choose to show/hide the route stop names).
if self.rsteps:
steps_dict = dict()
for step in self.rsteps:
# Add step to dictionary, if it doesn't exist.
steps_dict.setdefault(step.step_name, 0)
# Compute effective length.
if self.travel_mode != Travel_Mode.transit:
# For bike-only route, length is distance.
if step.edge_length is not None:
length_eff = step.edge_length
else:
length_eff = 0
else:
# For transit route, length is time.
if ((step.beg_time is not None)
and (step.fin_time is not None)):
length_eff = step.fin_time - step.beg_time
else:
length_eff = 0
# Aggregate effective length by step name.
steps_dict[step.step_name] += length_eff
# Find longest step.
max_len = 0
smart_name = ''
for step_name in steps_dict:
if steps_dict[step_name] > max_len:
max_len = steps_dict[step_name]
smart_name = step_name
# Finalise the smart name.
friendly_name = 'Route via %s' % (smart_name,)
else:
# This route doesn't have any route steps.
# Normally a route will have route steps. But if it doesn't...
# well, we could leave the route titled 'Untitled', or we could say
# something about this route not having any route steps.
# MAYBE: Use the names of the route stops?
log.warning('set_friendly_name: route has no steps')
friendly_name = 'Untitled (Empty Route)'
return friendly_name
#
def set_friendly_name(self):
self.name = self.get_friendly_name()
# ***
# ***
# FIXME: routes are supposed to be appended to the Many, not returned from
# search functions
class Many(geofeature.Many):
one_class = One
__slots__ = ()
sql_clauses_cols_all = geofeature.Many.sql_clauses_cols_all.clone()
# NOTE: Not sending z (z_level), since it's always the same value (160).
# MAGIC_NUMBER: 160 is route z-level.
sql_clauses_cols_all.inner.shared += (
"""
, rt.details
, rt.beg_addr
, rt.fin_addr
, rt.rsn_len
--, rt.travel_mode
, rt_ps.travel_mode
, rt_ps.p1_priority
, rt_ps.p2_depart_at
, rt_ps.p2_transit_pref
, rt_ps.p3_weight_attr
, rt_ps.p3_weight_type
, rt_ps.p3_rating_pump
, rt_ps.p3_burden_pump
, rt_ps.p3_spalgorithm
, rt_ps.tags_use_defaults
"""
)
# We shouldn't have to outer join route_parameters,
# but if it's missing any rows, than the client
# might be able spot errors, since we don't have
# any table constraints to protect us.
sql_clauses_cols_all.inner.join += (
"""
JOIN route AS rt
ON (gia.item_id = rt.system_id)
LEFT OUTER -- <--should be unnecessary
JOIN route_parameters AS rt_ps
ON ((gia.stack_id = rt_ps.route_stack_id)
AND (gia.branch_id = rt_ps.branch_id))
"""
)
sql_clauses_cols_all.outer.shared += (
"""
, group_item.details
, group_item.beg_addr
, group_item.fin_addr
, group_item.rsn_len
, group_item.travel_mode
, group_item.p1_priority
, group_item.p2_depart_at
, group_item.p2_transit_pref
, group_item.p3_weight_attr
, group_item.p3_weight_type
, group_item.p3_rating_pump
, group_item.p3_burden_pump
, group_item.p3_spalgorithm
, group_item.tags_use_defaults
""")
g.assurt(not sql_clauses_cols_all.outer.order_by)
# For route list pagination, order by last edited date.
sql_clauses_cols_all.outer.order_by = (
"""
edited_date DESC
""")
# **** SQL: Item version history query
# FIXME/BUG nnnn: Copy this to track.py when we make it revisionless.
# Also work_item, etc.
sql_clauses_cols_versions = (
item_revisionless.Many.sql_clauses_cols_versions_revisionless)
#sql_clauses_cols_versions = (
# item_revisionless.Many.sql_clauses_cols_versions_revisionless.clone())
# *** Constructor
def __init__(self):
geofeature.Many.__init__(self)
# *** Route-finding routines
#
def search_graph(self, req, routed, handler):
'''Finds a route from a beginning point (beg_xy) to a finishing point
(fin_xy). On success, stores the route in self.rsteps and
self.rstops; on error, including no route found, raises
GWIS_Error.'''
beg_xy = (handler.beg_ptx, handler.beg_pty,)
fin_xy = (handler.fin_ptx, handler.fin_pty,)
qb = None
rt = One(
qb,
row={
# Use a generic name for now. After computing the route, we'll fix
# the name so that it's more friendly.
'name': 'Untitled',
'geofeature_layer_id': Geofeature_Layer.Default,
'branch_id': req.branch.branch_id,
'z': 160, # MAGIC_NUMBER: 160 is route z-level.
#
# NOTE: The beg/fin addr friendly names are officially stored
# in route_stop rows (the first and last route stop for this
# route) but they're also cached in the route table (so we
# can get lists of routes quickly/easily).
'beg_addr': handler.beg_addr,
'fin_addr': handler.fin_addr,
# Set below: beg_nid, fin_nid
# Calculated later: rsn_len, rsn_min, rsn_max, n_steps, avg_cost
'travel_mode': handler.travel_mode,
# p1 planner:
'p1_priority': handler.p1_priority,
# p2 planner:
'p2_depart_at': handler.p2_depart_at,
'p2_transit_pref': handler.p2_transit_pref,
# p3 planner:
# Skipping: p3_weight_attr
'p3_weight_type': handler.p3_weight_type,
'p3_rating_pump': handler.p3_rating_pump,
'p3_burden_pump': handler.p3_burden_pump,
'p3_spalgorithm': handler.p3_spalgorithm,
# Personalized routing Tag preferences:
# Set next: tagprefs
'tags_use_defaults': handler.tags_use_defaults,
#
# Skipping: details (EXPLAIN: This is only used by mobile??
# Or it's only editable after a route
# is saved?)
# Skipping: stealth_secret (See item_stack table.)
# Skipping: created (set by setup_item_revisionless_defaults)
})
log.debug(
'search_graph: travel_mode: %s / route: %s'
% (Travel_Mode.lookup_by_id[handler.travel_mode], rt,))
rt.tagprefs = handler.tagprefs
try:
rating_func = routed.graph.ratings.rating_func(
req.client.username, rt.tagprefs, routed.graph)
except AttributeError:
# Graph class doesn't define ratings (i.e., p3 planner).
rating_func = None
qb = req.as_iqb()
# Debugging: just checking that the request didn't specify any viewport
# or other filters.
g.assurt(qb.viewport.include is None)
g.assurt(qb.viewport.exclude is None)
g.assurt(qb.filters == Query_Filters(None))
is_latlon = False
time_0 = time.time()
if handler.beg_nid is None:
# 2014.04.03: [lb] cannot find evidence that rating_min is
# set by the user. In route_get.py, it's set to 0.5.
src_by = One.byway_closest_xy(qb, rt.beg_addr, beg_xy,
rating_func, handler.rating_min,
is_latlon)
src_id = src_by.nearest_node_id()
else:
src_id = handler.beg_nid
rt.beg_nid = src_id
if handler.fin_nid is None:
dst_by = One.byway_closest_xy(qb, rt.fin_addr, fin_xy,
rating_func, handler.rating_min,
is_latlon)
dst_id = dst_by.nearest_node_id()
else:
dst_id = handler.fin_nid
rt.fin_nid = dst_id
log.info('search_graph: found node IDs in %s'
% (misc.time_format_elapsed(time_0),))
if src_id == dst_id:
# BUG nnnn: Honor m-values. If same m-value ret. x,y and draw a point.
raise GWIS_Warning('Locations given are too close to each other.')
if rt.travel_mode in Travel_Mode.p3_modes:
rt_finder = planner.routed_p3.route_finder.Problem(
req, routed.graph, rt)
elif rt.travel_mode in Travel_Mode.p2_modes:
# Calculate path using graphserver, which uses the simpler Dijkstra's.
is_reverse = False
rt_finder = planner.routed_p2.route_finder.Problem(
req, routed.graph, rt,
src_id, dst_id, rating_func, handler.rating_min,
beg_xy, fin_xy, is_reverse)
elif rt.travel_mode in Travel_Mode.p1_modes:
# Deprecated. Replaced by: Travel_Mode.personalized.
# But you can get here via Ccp.py still,
# and also route analysis. And via flashclient
# if you choose Classic Routes.
rt_finder = planner.routed_p1.route_finder.Problem(
req, routed.graph, rt,
src_id, dst_id, rating_func, handler.rating_min)
else:
g.assurt(False)
time_0 = time.time()
(rsteps, rstops, path_cost, path_len,) = rt_finder.solve(qb)
log.info(
'search_graph: found %d steps (%d stops) at %s cost (%s len) in %s'
% (len(rsteps), len(rstops), path_cost, path_len,
misc.time_format_elapsed(time_0),))
# The route finder raises GWIS_Warning if no route is found.
g.assurt(rsteps and rstops)
time_0 = time.time()
rt.rsteps = rsteps
rt.rstops = rstops
# Make a default friendly name according to the route steps (we figure
# out which byway is most used and use that in the name of the route).
rt.set_friendly_name()
if ((rt.avg_cost is None)
and ((handler.travel_mode != Travel_Mode.bicycle)
or (qb.username != conf.anonymous_username))):
if path_len:
rt.avg_cost = ((path_cost / route_step.One.weight_multiplier)
/ path_len)
log.debug('search_graph: 1 / rt.avg_cost: %s' % (rt.avg_cost,))
# else, we'll set avg_cost in either compute_stats_raw or
# savex_fetch_calculated_node_stats.
bonus_t = [t for t in rt.tagprefs if rt.tagprefs[t] == ratings.t_bonus]
penal_t = [t for t in rt.tagprefs if rt.tagprefs[t] == ratings.t_penalty]
cumulative_cost = None
if (((rt.avg_cost is None)
and (rating_func is not None)
and (rt.travel_mode == Travel_Mode.bicycle)
and (qb.username != conf.anonymous_username))
or (bonus_t)
or (penal_t)):
steps_total_len = 0.0
cumulative_cost = 0.0
for step in rt.rsteps:
if step.byway_stack_id:
# Lookup tags using the step cache.
step.bonus_tagged = routed.graph.byway_has_tags(
step.byway_stack_id, bonus_t)
step.penalty_tagged = routed.graph.byway_has_tags(
step.byway_stack_id, penal_t)
# SYNC_ME: Search edges...
if ((step.rating is None)
or (qb.username != conf.anonymous_username)):
try:
step.rating = rating_func(step.byway_stack_id)
except TypeError:
# rating_func is None.
# The route_step.One.init_from_shpfeat fcn. gets the
# average/generic rating for the byway, so that should
# be sufficient to return.
pass
# else, rating already set and user anonymous, so rating_func
# would just return the same value.
# FIXME/APRIL2014: Delete this else block or comment out after
# verifying (logcheck will complain if it hits, so, no logcheck
# complaints means it's okay to delete).
else:
anon_rating = rating_func(step.byway_stack_id)
if anon_rating != step.rating:
log.warning(
'rating dispute: step.rating: %s / anon_rating: %s'
% (step.rating, anon_rating,))
else:
log.warning('route step has no byway id?: %s' % (step,))
if rt.avg_cost is None:
step.calc_length_and_cost()
steps_total_len += step.edge_length
cumulative_cost += step.edge_weight
# end: for step in rt.rsteps
if rt.avg_cost is None:
if steps_total_len:
rt.avg_cost = (
(cumulative_cost / route_step.One.weight_multiplier)
/ steps_total_len)
log.debug('search_graph: 2 / rt.avg_cost: %s' % (rt.avg_cost,))
# else, we'll set avg_cost in either compute_stats_raw or
# savex_fetch_calculated_node_stats.
# An all_bike_path is from p1 or p3, i.e., not the p2 multimodal planner.
all_bike_path = True
for step in rt.rsteps:
if step.travel_mode != Travel_Mode.bicycle:
all_bike_path = False
break
if all_bike_path and (rt.travel_mode == Travel_Mode.transit):
# If the route came from routed_p2 but is all bike paths, adjust
# its travel mode so that it will function like an editable route.
# BUG nnnn: When the user chooses to edit this route, the fact that it
# was a transit route will be lost. When user's choose
# to edit a route, can they use the Metro Transit
# checkbox? Would this imply creating/cloning the route?
# For now, we could just tell the user with a popup or
# alert.
rt.travel_mode = Travel_Mode.bicycle
#rt.travel_mode = Travel_Mode.wayward
log.info('search_graph: iterated over step ratings in %s'
% (misc.time_format_elapsed(time_0),))
log.debug(
'search_graph: found rte: %d steps / %d stops / %s'
% (len(rsteps),
len(rstops),
'path_cost: %s / path_len: %s / cuml_cost: %s / avg_cost: %s'
% ('None' if path_cost is None
else '%.2f' % (path_cost,),
'None' if path_len is None
else '%.2f' % (path_len,),
'None' if cumulative_cost is None
else '%.2f' % (cumulative_cost,),
'None' if rt.avg_cost is None
else '%.2f' % (rt.avg_cost,),),))
# Return the fresh, invalid route (invalid because it's up to the caller
# to prepare the item for saving and then save it, if they so desire).
return rt
# *** Query Builder routines
# MAYBE: In CcpV1, there's a search_by_rquery you can use to find routes by
# geometry. [lb] isn't quite remembering how exactly it worked... but
# is it something maybe we want to implement again?
# E.g.,
# def search_by_rquery(self, req, username, rquery, vquery):
# ...
# # HACK: route's historic query does not work like most map features
# # so Historic has a special flag that can be turned on to change
# # it's behavior
# if isinstance(vquery, revision_query.Historic):
# vquery.is_route = True
#
# where_user = '''(visibility = 1 OR (visibility = 2
# AND owner_name IS NOT NULL
# AND owner_name = %s))''' % (req.db.quoted(username))
#
# rows = req.db.sql(
# """
# SELECT id, version
# FROM route_geo rg
# WHERE %s
# AND %s
# AND %s
# """ % (where_user,
# rquery.as_sql_where(vquery, 'route_geo', 'rg'),
# vquery.as_sql_where(),))
#
# for row in rows:
# self.add(self.search_by_id(req, row['id'], row['version']))
#
def search_by_stack_id(self, stack_id, *args, **kwargs):
qb = self.query_builderer(*args, **kwargs)
geofeature.Many.search_by_stack_id(self, stack_id, qb)
# ***
#
def search_get_sql(self, qb):
# Forever, and always. We always sort routes by edited_date,
# so we always need to set include_item_stack.
qb.filters.include_item_stack = True
sql = geofeature.Many.search_get_sql(self, qb)
return sql
#
def search_get_items(self, qb):
geofeature.Many.search_get_items(self, qb)
# Skipping: qb.filters.dont_load_route_details
if (not qb.db.dont_fetchall) and (qb.filters.include_item_aux):
self.routes_load_aux(qb)
# else, see search_for_items_clever and search_get_items_add_item_cb.
#
def search_for_items_clever(self, *args, **kwargs):
qb = self.query_builderer(*args, **kwargs)
g.assurt(not qb.db.dont_fetchall)
geofeature.Many.search_for_items_clever(self, qb)
if qb.filters.include_item_aux:
self.routes_load_aux(qb)
#
def search_for_items_diff(self, qb):
raise GWIS_Error('Diff checkout not supported for routes.')
#
def search_for_items_load(self, qb, diff_group):
# To get an historic version of restricted-access items, use
# revision.Comprehensive.
g.assurt(isinstance(qb.revision, revision.Current))
geofeature.Many.search_for_items_load(self, qb, diff_group)
#
def sql_apply_query_filters_item_stack_revisiony(self, qb, use_inner_join):
# Routes, tracks, posts, threads, oh my, are revisionless.
self.sql_apply_query_filters_item_stack_revisionless(qb, use_inner_join)
#
def sql_apply_query_filters_last_editor(self, qb, where_clause,
conjunction):
# NOTE: Not calling geofeature.Many.sql_apply_query_filters_last_editor.
# We got this.
# FIXME: Copy this fcn. to track, when we make tracks revisionless.
# Or derive route and track from common ancestor.
return self.sql_apply_query_filters_last_editor_revisionless(qb,
where_clause, conjunction)
#
def sql_enabled_squelch_circuitry(self):
# Refer to the item_findability table when searching for non-specific
# items.
return True
# ***
#
def routes_load_aux(self, qb):
# Routes are special objects that require a lot more manual loading.
# SYNC_ME: route.routes_load_aux and track.tracks_load_aux.
# NOTE/FIXME: routes are branch-specific, so
# WHERE stack_id= AND branch_id=
# is not really needed (and maybe misleading?).
# NOTE: Starting with rtsharing, routes are versioned, but that
# doesn't matter for route_parameters and route_tag_preference, since
# those values are set just once.
routes_aux_limit = 1
if len(self) > routes_aux_limit:
log.warning("More than %d routes found: ignoring %d routes' aux data"
% (routes_aux_limit, (len(self) - routes_aux_limit),))
elif len(self) == 0:
log.debug('routes_load_aux: no routes: %s' % (str(self),))
routes = self[0:routes_aux_limit]
for rt in routes:
# Route stops.
rows = qb.db.sql(
"""
SELECT
stop_number,
name,
x,
y,
node_id,
is_pass_through,
is_transit_stop,
internal_system_id,
external_result
FROM
route_stop
WHERE
route_id = %d
ORDER BY
stop_number ASC
""" % (rt.system_id,))
for row in rows:
rt.rstops.append(route_stop.One(qb, row=row))
# Tag preferences (tag_preference table)
rt.fill_tagprefs(qb)
# Route steps (route_step table)
rt.fill_path(qb)
# Fix route stops with empty node IDs.
# BUG nnnn: Routed p2: Editable routes.
route_step.Many.repair_node_ids(qb, rt.rsteps)
# The route is now completed, and it's already been appended to
# self (Many) so we can continue looping over the routes (though
# it's unlikely to be more than one).
# *** Table management
indexed_cols = (
#'rsn_min', # The first step_number; BUGBUG: not always 0.
#'rsn_max', # The last step_number, since a few gaps have
# # gaps in their route_step sequence.
#'n_steps', # Number of route_step rows for this route.
#'rsn_len', #
'beg_nid', # The beginning node endpoint.
'fin_nid', # The finishing node endpoint.
)
#
@staticmethod
def drop_indices(db):
# FIXME: This loop shared by the node_ classes. Put in some base class.
for col_name in Many.indexed_cols:
db.sql("DROP INDEX IF EXISTS route_%s" % (col_name,))
#
@staticmethod
def make_indices(db):
# Drop the indices first.
Many.drop_indices(db)
# Re(make) the indices.
for col_name in Many.indexed_cols:
db.sql("CREATE INDEX route_%s ON route(%s)"
% (col_name, col_name,))
# ***
#
# MAYBE: This gets called whenever the route is saved, even if it's just
# that the user made a stealth secret and we just had to make a GIA record.
@staticmethod
def update_node_stats(qb, system_id=None,
stack_id=None,
all_routes=False,
prog_log=None):
if system_id:
g.assurt(not (stack_id or all_routes))
where_clause = "WHERE rt.system_id = %d" % (system_id,)
elif stack_id:
g.assurt(not (system_id or all_routes))
where_clause = "WHERE rt.stack_id = %d" % (stack_id,)
else:
g.assurt(not (stack_id or system_id))
where_clause = ""
# We don't have to worry about the revision because we group things by
# route system ID, and its route_steps have the system IDs of byways --
# and system IDs are inherently revisiony.
# MAYBE: NOTE: Some routes in the database are inconsistent. Some have
# missing route_step rows (i.e., there are missing route_numbers) and
# some don't start on 0, which is supposed to be the first index.
#first_index = 0
# NOTE: To calculate beg_addr and fin_addr, we could make an inner select
# that calculates the min() and max() stop_numbers for the route and use
# that to join against route_stop (like we do for beg_nid and
# fin_nid), or we could do a select in the select list and use order-by
# to get the rows we want (a trick first writ by [ml]).
# FIXME: wrong: you need to iterate one route at a time, dummy.
# or else the new outer join totally slowed this down...
# or maybe i'm not patient
# this is taking almost a halh hour now -- you should do route IDs, then at
# least you can test what's taking so long (prob. scratch space! maybe this
# runs fast if you have the mem)
# FIXME: transit_geometry and geometry. Maybe rename geometry to
# byway_geometry? Or move both to a single geometry column and use
# a boolean to indicate that its transit (or rely on NULL byway_id?)?
routes_sql = (
"""
SELECT
--
foo_rte_1.system_id
--
, (SELECT name FROM route_stop AS rw
WHERE rw.route_id = foo_rte_1.system_id
ORDER BY rw.stop_number ASC LIMIT 1) AS beg_addr
, (SELECT name FROM route_stop AS rw
WHERE rw.route_id = foo_rte_1.system_id
ORDER BY rw.stop_number DESC LIMIT 1) AS fin_addr
--
, rs_beg.forward AS lhs_forward
, gf_beg.beg_node_id AS lhs_beg_node_id
, gf_beg.fin_node_id AS lhs_fin_node_id
--
, rs_fin.forward AS rhs_forward
, gf_fin.beg_node_id AS rhs_beg_node_id
, gf_fin.fin_node_id AS rhs_fin_node_id
--
, foo_rte_1.step_count_min
, foo_rte_1.step_count_max
, foo_rte_1.step_count_count
--
--, foo_rte_1.steps_total_len
/* FIXME: I don't know that we need to correct reversed line
segments...
, (SELECT ST_Length(
SELECT ST_Collect(
SELECT
CASE
WHEN rs.transit_geometry IS NOT NULL
THEN rs.transit_geometry
ELSE (
SELECT
CASE
WHEN rs.forward THEN gf.geometry
ELSE ST_Reverse(gf.geometry)
END AS geometry
FROM geofeature AS gf
WHERE gf.system_id = rs.byway_id)
END AS geometry
FROM route_step AS rs
WHERE (rs.route_id = foo_rte_1.system_id)))
) AS steps_total_len
*/
--, ST_Length(ST_Collect(collected_geo_geo, collected_geo_tx))
-- AS steps_total_len
, CASE
WHEN collected_geo_geo is NOT NULL THEN
ST_Length(ST_Collect(collected_geo_geo, collected_geo_tx))
ELSE
-- FIXME: Is this right? 0?
0
END AS steps_total_len
/* Get the system ID and step count using an inner query. */
FROM (
SELECT
rt.system_id
, MIN(rs.step_number) AS step_count_min
, MAX(rs.step_number) AS step_count_max
, COUNT(rs.step_number) AS step_count_count
--, ST_Collect(rs.geometry) AS collected_geo_geo
, ST_Collect(gf_inner.geometry) AS collected_geo_geo
, ST_Collect(rs.transit_geometry) AS collected_geo_tx
FROM
route AS rt
JOIN
route_step AS rs
ON (rt.system_id = rs.route_id)
LEFT OUTER JOIN
geofeature AS gf_inner
ON (rs.byway_id = gf_inner.system_id)
%s -- WHERE
GROUP BY
rt.system_id
) AS foo_rte_1
/* First route_step and its byway. */
JOIN
route_step AS rs_beg
ON ((foo_rte_1.system_id = rs_beg.route_id)
AND (rs_beg.step_number = foo_rte_1.step_count_min))
JOIN
geofeature AS gf_beg
ON (rs_beg.byway_id = gf_beg.system_id)
/* Last route_step and its byway. */
JOIN
route_step AS rs_fin
ON ((foo_rte_1.system_id = rs_fin.route_id)
AND (rs_fin.step_number = foo_rte_1.step_count_max))
JOIN
geofeature AS gf_fin
ON (rs_fin.byway_id = gf_fin.system_id)
""" % (where_clause,))
if not where_clause:
logl = log.info
else:
# MAYBE: log.verbose
logl = log.debug
# This takes a while when searching all routes!
# 2012.07.11: Raw SQL: 102474 rows in 4-1/3 mins.
# 2012.07.11: LIMIT 1: 1 row in 5360.518 ms.
# 2012.07.13: From node_cache_maker: 102587 in 0.9.
logl('update_node_stats: searching for routes...')
sole_row = None
time_0 = time.time()
try:
db = qb.db.clone()
db.dont_fetchall = True
db.sql(routes_sql)
if db.curs.rowcount <= 0:
log.warning('update_node_stats: no routes found: %d'
% (db.curs.rowcount,))
else:
log.info('Found %d routes in %s'
% (db.curs.rowcount,
misc.time_format_elapsed(time_0),))
time_0 = time.time()
try:
another_db = db.clone()
#another_db.transaction_begin_rw()
sole_row = Many.update_node_stats_process(
db, another_db, prog_log)
finally:
another_db.close()
log.info('update_node_stats_process: in %s'
% (misc.time_format_elapsed(time_0),))
finally:
log.verbose('update_node_stats: disabling dont_fetchall')
db.dont_fetchall = False
#db.curs_recycle()
db.close()
return sole_row
#
@staticmethod
def update_node_stats_process(db, another_db, prog_log=None):
log.info('Processing routes and updating table...')
sole_row = None
step_count_exact = 0
step_count_holey = 0
step_count_later = 0
step_count_buckets = {}
if prog_log is None:
prog_log = Debug_Progress_Logger()
prog_log.log_listen = None
prog_log.log_silently = True
prog_log.loop_max = db.curs.rowcount
if prog_log.log_freq == 1:
prog_log.log_freq = 1000
# MAGIC NUMBER: I'm just guessing here. Testing new idea: bulk UPDATEs.
update_freq = 1000
g.assurt(update_freq > 0)
# Reset the bulk collection.
updates = []
generator = db.get_row_iter()
for row in generator:
# Get the columns.
#
system_id = row['system_id']
#
beg_addr = row['beg_addr']
fin_addr = row['fin_addr']
#
lhs_forward = row['lhs_forward']
lhs_beg_node_id = row['lhs_beg_node_id']
lhs_fin_node_id = row['lhs_fin_node_id']
#
rhs_forward = row['rhs_forward']
rhs_beg_node_id = row['rhs_beg_node_id']
rhs_fin_node_id = row['rhs_fin_node_id']
#
step_count_min = row['step_count_min']
step_count_max = row['step_count_max']
step_count_count = row['step_count_count']
#
steps_total_len = row['steps_total_len']
# The step_column value is 0-based, non-negative, and incremental.
# 2012.07.13: EXPLAIN: Why are there missing step_numbers in the
# table? I.e.,
# select * from route where system_id = 234872;
# select * from route_step where route_id = 234872;
# NOT ALWAYS TRUE: g.assurt(step_count_max == (step_count_count - 1))
if step_count_max == (step_count_count - 1):
step_count_exact += 1
else:
g.assurt(step_count_max >= (step_count_count - 1))
step_count_holey += 1
#
if step_count_min > 0:
step_count_later += 1
#
misc.dict_count_inc(step_count_buckets, step_count_count)
if lhs_forward:
rte_beg_node_id = lhs_beg_node_id
else:
rte_beg_node_id = lhs_fin_node_id
#
# 2014.09.11: Should'nt the order be reversed here?
# Or don't we have enough information to
# know which node is closer to the user's
# true destination?
# if rhs_forward:
# rte_fin_node_id = rhs_beg_node_id
# else:
# rte_fin_node_id = rhs_fin_node_id
if rhs_forward:
rte_fin_node_id = rhs_fin_node_id
else:
rte_fin_node_id = rhs_beg_node_id
# Save a tuple to the update list.
updates.append("(%d, %s, %s, %d, %d, %d, %.1f, %d, %d)"
% (system_id,
db.quoted(beg_addr),
db.quoted(fin_addr),
step_count_min, # rsn_min
step_count_max, # rsn_max
step_count_count, # n_steps
steps_total_len, # rsn_len
rte_beg_node_id, # beg_node_id
rte_fin_node_id, # fin_node_id
))
# We only update every so often.
if prog_log.progress % update_freq == 0:
# Time to bulk-update.
# NOTE: Using qb's db, not the cloned one we're using to fetchone.
Many.node_bulk_update(another_db, updates)
# Reset the update list.
updates = []
if db.curs.rowcount == 1:
sole_row = row
# If debugging, break early maybe.
if prog_log.loops_inc():
break
# end: for row in generator
if generator is not None:
generator.close()
generator = None
# One last time.
if updates:
# NOTE: Again using qb's db and not our local clone.
Many.node_bulk_update(another_db, updates)
updates = []
log.info('update_node_stats: good step_count seqs.: %d'
% (step_count_exact,))
log.info(' w/ gaps in the sequence: %d'
% (step_count_holey,))
log.info(' w/ first step_number > 0: %d'
% (step_count_later,))
keys = step_count_buckets.keys()
#keys.sort()
#for step_count in keys:
for key_i in xrange(len(keys)):
try:
step_count = keys[key_i]
# Only output the last few route stats or any short routes.
if (step_count < 3) or (key_i >= (len(keys) - 2)):
route_ct = step_count_buckets[step_count]
log.info(' No. of Routes with %03d route_steps: %d'
% (step_count, route_ct,))
except KeyError:
pass
prog_log.loops_fin(callee='update_node_stats')
return sole_row
#
@staticmethod
def node_bulk_update(another_db, updates):
g.assurt(updates)
# Format is, e.g.,
# UPDATE
# tbl_1
# SET
# col1 = t.col1
# FROM (
# VALUES
# (25, 3)
# (26, 5)
# ) AS t(id, col1)
# WHERE tbl_1.id = t.id;
update_sql = (
"""
UPDATE
route
SET
beg_addr = foo_rte_2.beg_addr
, fin_addr = foo_rte_2.fin_addr
, rsn_min = foo_rte_2.rsn_min
, rsn_max = foo_rte_2.rsn_max
, n_steps = foo_rte_2.n_steps
, rsn_len = foo_rte_2.rsn_len
, beg_nid = foo_rte_2.beg_node_id
, fin_nid = foo_rte_2.fin_node_id
FROM
(VALUES %s) AS foo_rte_2(system_id,
beg_addr,
fin_addr,
rsn_min,
rsn_max,
n_steps,
rsn_len,
beg_node_id,
fin_node_id)
WHERE
route.system_id = foo_rte_2.system_id
""" % (','.join(updates),))
another_db.sql(update_sql)
# ***
# ***
|
lbouma/Cyclopath
|
pyserver/item/feat/route.py
|
Python
|
apache-2.0
| 99,604
|
[
"VisIt"
] |
3aabebf13a6a62ea299acae7e5af2b514a8b0f0f5f2bf8c2345bf25fcb0e08fb
|
#!/usr/bin/env python
# coding=utf-8
from distutils.core import setup
from setuptools import find_packages
PACKAGE = "lightnn"
NAME = "lightnn"
DESCRIPTION = "This package can download funds data from https://github.com/l11x0m7/lightnn. For details, please visit https://skyhigh233.com."
AUTHOR = "Xuming Lin"
AUTHOR_EMAIL = "l11x0m7@gmail.com"
URL = "https://github.com/l11x0m7/lightnn"
VERSION = __import__(PACKAGE).__version__
setup(
name=NAME,
version=VERSION,
description=DESCRIPTION,
# long_description=open("README.md", 'rb').readlines(),
author=AUTHOR,
author_email=AUTHOR_EMAIL,
license="Apache License, Version 2.0",
url=URL,
packages=find_packages('./'),
classifiers=[
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Operating System :: OS Independent",
"Programming Language :: Python",
],
zip_safe=False,
)
|
l11x0m7/lightnn
|
setup.py
|
Python
|
apache-2.0
| 1,091
|
[
"VisIt"
] |
edb16622c8c45efbb4c71c87f4aaed938c32a8353a66376640334eed9a450418
|
"""
Implements various interpreters and modders for VASP.
"""
from pymatgen.io.vasp.inputs import VaspInput
from custodian.ansible.actions import DictActions, FileActions
from custodian.ansible.interpreter import Modder
class VaspModder(Modder):
"""
A Modder for VaspInputSets.
"""
def __init__(self, actions=None, strict=True, vi=None):
"""
Initializes a Modder for VaspInput sets
Args:
actions ([Action]): A sequence of supported actions. See
:mod:`custodian.ansible.actions`. Default is None,
which means DictActions and FileActions are supported.
strict (bool): Indicating whether to use strict mode. In non-strict
mode, unsupported actions are simply ignored without any
errors raised. In strict mode, if an unsupported action is
supplied, a ValueError is raised. Defaults to True.
vi (VaspInput): A VaspInput object from the current directory.
Initialized automatically if not passed (but passing it will
avoid having to reparse the directory).
"""
self.vi = vi or VaspInput.from_directory(".")
actions = actions or [FileActions, DictActions]
super().__init__(actions, strict)
def apply_actions(self, actions):
"""
Applies a list of actions to the Vasp Input Set and rewrites modified
files.
Args:
actions [dict]: A list of actions of the form {'file': filename,
'action': moddermodification} or {'dict': vaspinput_key,
'action': moddermodification}
"""
modified = []
for a in actions:
if "dict" in a:
k = a["dict"]
modified.append(k)
self.vi[k] = self.modify_object(a["action"], self.vi[k])
elif "file" in a:
self.modify(a["action"], a["file"])
else:
raise ValueError(f"Unrecognized format: {a}")
for f in modified:
self.vi[f].write_file(f)
|
materialsproject/custodian
|
custodian/vasp/interpreter.py
|
Python
|
mit
| 2,115
|
[
"VASP",
"pymatgen"
] |
2ad64553bc1cf0fa1ff3d24f2008f6dcd254dda17321b29fa3d9728ffd36afd3
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
dimensions= 1
size1d = 30
halfSize1 = [size1d,0.2,0.1]
halfSize2 = halfSize1
GRIDSIZE = 256
# wavepacket parameters
k0_x = 0
k0_y = 0
gaussWidth_x = 1.0
gaussWidth_y = 0.0
potentialCoefficient1= [-2.0,0.5,0.5]
potentialCoefficient2= [ 2.0,0.5,0.5]
O.engines=[
StateDispatcher([
St1_QMPacketGaussianWave(),
]),
SpatialQuickSortCollider([
Bo1_Box_Aabb(),
]),
InteractionLoop(
[Ig2_2xQMGeometry_QMIGeom()],
[Ip2_QMParticleCoulomb_QMParticleCoulomb_QMIPhysCoulombParticles()],
[Law2_QMIGeom_QMIPhysCoulombParticles()]
),
SchrodingerKosloffPropagator(),
]
displayEnt= { 'partAbsolute':['default surface', 'hidden', 'nodes', 'points', 'wire', 'surface']
,'partImaginary':['default hidden', 'hidden', 'nodes', 'points', 'wire', 'surface']
,'partReal':['default hidden', 'hidden', 'nodes', 'points', 'wire', 'surface']
,'stepRender':["default hidden","hidden","frame","stripes","mesh"]
}
body0 = QMBody()
body0.shape = QMGeometry(extents=halfSize1,color=[0.8,0.8,0.8],displayOptions=[
QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False ,renderSe3=(Vector3(-size1d*1.2, 0,0), Quaternion((1,0,0),0)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False ,renderSe3=(Vector3(-size1d*1.2, size1d,0), Quaternion((1,0,0),0)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False ,renderSe3=(Vector3(-size1d*1.2,-size1d,0), Quaternion((1,0,0),0)) )
,QMDisplayOptions(partsScale=10,partsSquared=True,renderWireLight=True ,renderSe3=(Vector3(-size1d*1.2, 0,0), Quaternion((1,0,0),0))
,doMarginalDistribution=[(0,0,0),(0,0,0)],**displayEnt)
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False,renderFFT=True ,renderSe3=(Vector3(size1d*1.2, 0,0), Quaternion((1,0,0),0)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False,renderFFT=True ,renderSe3=(Vector3(size1d*1.2, size1d,0), Quaternion((1,0,0),0)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False,renderFFT=True ,renderSe3=(Vector3(size1d*1.2,-size1d,0), Quaternion((1,0,0),0)) )
,QMDisplayOptions(partsScale=10,partsSquared=True,renderWireLight=True ,renderFFT=True ,renderSe3=(Vector3(size1d*1.2, 0,0), Quaternion((1,0,0),0))
, doMarginalDistribution=[(0,0,0),(0,0,0)],**displayEnt)
# ,renderSe3=(Vector3(0,0,-4), Quaternion((1,0,0),0))
# ,renderFFTScale=(4,1,1)
])
body0.material = QMParticleCoulomb(dim=dimensions,hbar=1,m=1,coefficient=potentialCoefficient1)
# FFTW is best at handling sizes of the form 2ᵃ 3ᵇ 5ᶜ 7ᵈ 11ᵉ 13ᶠ , where e+f is either 0 or 1 ## http://www.nanophys.kth.se/nanophys/fftw-info/fftw_3.html
body0.state = QMPacketGaussianWave(x0=[-1,0,0],t0=0,k0=[k0_x,k0_y,0],a0=[gaussWidth_x,gaussWidth_y,0],gridSize=[GRIDSIZE]) #,se3=[[0.5,0.5,0.5],Quaternion((1,0,0),0)])
nid=O.bodies.append(body0)
O.bodies[nid].state.setNumeric()
body1 = QMBody()
body1.shape = QMGeometry(extents=halfSize2,color=[1,1,1],displayOptions=[
QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False ,renderSe3=(Vector3(-size1d*1.2 ,0,0), Quaternion((0,0,1),0 )) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False ,renderSe3=(Vector3(-size1d*1.2+size1d,0,0), Quaternion((0,0,1),pi/2)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False ,renderSe3=(Vector3(-size1d*1.2-size1d,0,0), Quaternion((0,0,1),pi/2)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False,renderFFT=True ,renderSe3=(Vector3(size1d*1.2 ,0,0), Quaternion((1,0,0),0 )) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False,renderFFT=True ,renderSe3=(Vector3(size1d*1.2+size1d,0,0), Quaternion((0,0,1),pi/2)) )
,QMDisplayOptions(partsScale=10,partsSquared=False,renderWireLight=False,renderFFT=True ,renderSe3=(Vector3(size1d*1.2-size1d,0,0), Quaternion((0,0,1),pi/2)) )
])
body1.material = QMParticleCoulomb(dim=dimensions,hbar=1,m=1,coefficient=potentialCoefficient2)
## FIXME - przetestować w mathematica z różnie przesuniętymi względem siebie siatkami i różnym rozstawem siatek.
## głównie chodzi o to, żeby węzły siatek się nie nakrywały.
body1.state = QMPacketGaussianWave(x0=[1,0,0],t0=0,k0=[-k0_x,-k0_y,0],a0=[gaussWidth_x,gaussWidth_y,0],gridSize=[GRIDSIZE]) #,se3=[[0.5,0.5,0.5],Quaternion((1,0,0),0)])
nid=O.bodies.append(body1)
O.bodies[nid].state.setNumeric()
O.dt=.02
O.save('/tmp/a.xml.bz2');
#o.run(100000); o.wait(); print o.iter/o.realtime,'iterations/sec'
try:
from yade import qt
qt.Controller()
qt.controller.setWindowTitle("Two Gaussian packets connected via Coulomb potential in 1D")
qt.Renderer().blinkHighlight=False
qt.View()
qt.controller.setViewAxes(dir=(0,1,0),up=(0,0,1))
qt.views()[0].center(False,10) # median=False, suggestedRadius = 5
except ImportError:
pass
#O.run(20000)
#### save result for comparison with mathematica
#
# nn=O.bodies[0].state
# ff=open("1d-harmonic-interaction-yade.txt",'w')
# for i in range(nn.gridSize[0]):
# ff.write(str(nn.iToX(i,0))+" "+str(nn.iToX(96,1))+" "+str((nn.atPsiGlobal([i,96])).real)+" "+str((nn.atPsiGlobal([i,96])).imag)+"\n")
# ff.close()
#Yade [3]: def zapisz(nazwa,x2):
# ...: nn=O.bodies[0].state
# ...: ff=open(nazwa,'w')
# ...: for i in range(nn.gridSize[0]):
# ...: ff.write(str(nn.iToX(i,0))+" "+str(nn.iToX(x2,1))+" "+str((nn.atPsiGlobal([i,x2])).real)+" "+str((nn.atPsiGlobal([i,x2])).imag)+"\n")
# ...: ff.close()
# ...:
#zapisz("1d-harmonic-interaction-yade_0.05_506.txt",506)
#zapisz("1d-harmonic-interaction-yade_0.05_507.txt",507)
#zapisz("1d-harmonic-interaction-yade_0.05_508.txt",508)
#zapisz("1d-harmonic-interaction-yade_0.05_509.txt",509)
#zapisz("1d-harmonic-interaction-yade_0.05_510.txt",510)
#zapisz("1d-harmonic-interaction-yade_0.05_511.txt",511)
#zapisz("1d-harmonic-interaction-yade_0.05_512.txt",512)
#zapisz("1d-harmonic-interaction-yade_0.05_513.txt",513)
#zapisz("1d-harmonic-interaction-yade_0.05_514.txt",514)
#zapisz("1d-harmonic-interaction-yade_0.05_515.txt",515)
#zapisz("1d-harmonic-interaction-yade_0.05_516.txt",516)
#zapisz("1d-harmonic-interaction-yade_0.05_517.txt",517)
#zapisz("1d-harmonic-interaction-yade_0.05_518.txt",518)
#zapisz("1d-harmonic-interaction-yade_0.1_506.txt",506)
#zapisz("1d-harmonic-interaction-yade_0.1_507.txt",507)
#zapisz("1d-harmonic-interaction-yade_0.1_508.txt",508)
#zapisz("1d-harmonic-interaction-yade_0.1_509.txt",509)
#zapisz("1d-harmonic-interaction-yade_0.1_510.txt",510)
#zapisz("1d-harmonic-interaction-yade_0.1_511.txt",511)
#zapisz("1d-harmonic-interaction-yade_0.1_512.txt",512)
#zapisz("1d-harmonic-interaction-yade_0.1_513.txt",513)
#zapisz("1d-harmonic-interaction-yade_0.1_514.txt",514)
#zapisz("1d-harmonic-interaction-yade_0.1_515.txt",515)
#zapisz("1d-harmonic-interaction-yade_0.1_516.txt",516)
#zapisz("1d-harmonic-interaction-yade_0.1_517.txt",517)
#zapisz("1d-harmonic-interaction-yade_0.1_518.txt",518)
# gnuplot
#N="./1d-harmonic-interaction-yade_0."
#M="./1d-harmonic-interaction-mathematica_0."
#set grid
#set xtics 1
#t=512
#plot N."05_".sprintf("%.3i",t).".txt" u 1:3 w l lt 1,N."05_".sprintf("%.3i",t).".txt" u 1:4 w l lt 2,M."05_".sprintf("%.3i",t).".txt" u 1:3 w l lt 3,M."05_".sprintf("%.3i",t).".txt" u 1:4 w l lt 4 title sprintf("%.3i",t)
#plot N."1_".sprintf("%.3i",t).".txt" u 1:3 w l lt 1,N."1_".sprintf("%.3i",t).".txt" u 1:4 w l lt 2,M."1_".sprintf("%.3i",t).".txt" u 1:3 w l lt 3,M."1_".sprintf("%.3i",t).".txt" u 1:4 w l lt 4 title sprintf("%.3i",t)
#
|
cosurgi/trunk
|
examples/qm/1d-coulomb-interaction.py
|
Python
|
gpl-2.0
| 7,851
|
[
"Gaussian"
] |
cda8bab9ff0bcb348eb061d10160a95c22aa59b931ef1b814292a15b310d2e0d
|
# -*- coding: utf-8 -*-
"""
======================
Laplacian segmentation
======================
This notebook implements the laplacian segmentation method of
`McFee and Ellis, 2014 <http://bmcfee.github.io/papers/ismir2014_spectral.pdf>`_,
with a couple of minor stability improvements.
Throughout the example, we will refer to equations in the paper by number, so it will be
helpful to read along.
"""
# Code source: Brian McFee
# License: ISC
###################################
# Imports
# - numpy for basic functionality
# - scipy for graph Laplacian
# - matplotlib for visualization
# - sklearn.cluster for K-Means
#
import numpy as np
import scipy
import matplotlib.pyplot as plt
import sklearn.cluster
import librosa
import librosa.display
#############################
# First, we'll load in a song
y, sr = librosa.load(librosa.ex('fishin'))
##############################################
# Next, we'll compute and plot a log-power CQT
BINS_PER_OCTAVE = 12 * 3
N_OCTAVES = 7
C = librosa.amplitude_to_db(np.abs(librosa.cqt(y=y, sr=sr,
bins_per_octave=BINS_PER_OCTAVE,
n_bins=N_OCTAVES * BINS_PER_OCTAVE)),
ref=np.max)
fig, ax = plt.subplots()
librosa.display.specshow(C, y_axis='cqt_hz', sr=sr,
bins_per_octave=BINS_PER_OCTAVE,
x_axis='time', ax=ax)
##########################################################
# To reduce dimensionality, we'll beat-synchronous the CQT
tempo, beats = librosa.beat.beat_track(y=y, sr=sr, trim=False)
Csync = librosa.util.sync(C, beats, aggregate=np.median)
# For plotting purposes, we'll need the timing of the beats
# we fix_frames to include non-beat frames 0 and C.shape[1] (final frame)
beat_times = librosa.frames_to_time(librosa.util.fix_frames(beats,
x_min=0,
x_max=C.shape[1]),
sr=sr)
fig, ax = plt.subplots()
librosa.display.specshow(Csync, bins_per_octave=12*3,
y_axis='cqt_hz', x_axis='time',
x_coords=beat_times, ax=ax)
#####################################################################
# Let's build a weighted recurrence matrix using beat-synchronous CQT
# (Equation 1)
# width=3 prevents links within the same bar
# mode='affinity' here implements S_rep (after Eq. 8)
R = librosa.segment.recurrence_matrix(Csync, width=3, mode='affinity',
sym=True)
# Enhance diagonals with a median filter (Equation 2)
df = librosa.segment.timelag_filter(scipy.ndimage.median_filter)
Rf = df(R, size=(1, 7))
###################################################################
# Now let's build the sequence matrix (S_loc) using mfcc-similarity
#
# :math:`R_\text{path}[i, i\pm 1] = \exp(-\|C_i - C_{i\pm 1}\|^2 / \sigma^2)`
#
# Here, we take :math:`\sigma` to be the median distance between successive beats.
#
mfcc = librosa.feature.mfcc(y=y, sr=sr)
Msync = librosa.util.sync(mfcc, beats)
path_distance = np.sum(np.diff(Msync, axis=1)**2, axis=0)
sigma = np.median(path_distance)
path_sim = np.exp(-path_distance / sigma)
R_path = np.diag(path_sim, k=1) + np.diag(path_sim, k=-1)
##########################################################
# And compute the balanced combination (Equations 6, 7, 9)
deg_path = np.sum(R_path, axis=1)
deg_rec = np.sum(Rf, axis=1)
mu = deg_path.dot(deg_path + deg_rec) / np.sum((deg_path + deg_rec)**2)
A = mu * Rf + (1 - mu) * R_path
###########################################################
# Plot the resulting graphs (Figure 1, left and center)
fig, ax = plt.subplots(ncols=3, sharex=True, sharey=True, figsize=(10, 4))
librosa.display.specshow(Rf, cmap='inferno_r', y_axis='time', x_axis='s',
y_coords=beat_times, x_coords=beat_times, ax=ax[0])
ax[0].set(title='Recurrence similarity')
ax[0].label_outer()
librosa.display.specshow(R_path, cmap='inferno_r', y_axis='time', x_axis='s',
y_coords=beat_times, x_coords=beat_times, ax=ax[1])
ax[1].set(title='Path similarity')
ax[1].label_outer()
librosa.display.specshow(A, cmap='inferno_r', y_axis='time', x_axis='s',
y_coords=beat_times, x_coords=beat_times, ax=ax[2])
ax[2].set(title='Combined graph')
ax[2].label_outer()
#####################################################
# Now let's compute the normalized Laplacian (Eq. 10)
L = scipy.sparse.csgraph.laplacian(A, normed=True)
# and its spectral decomposition
evals, evecs = scipy.linalg.eigh(L)
# We can clean this up further with a median filter.
# This can help smooth over small discontinuities
evecs = scipy.ndimage.median_filter(evecs, size=(9, 1))
# cumulative normalization is needed for symmetric normalize laplacian eigenvectors
Cnorm = np.cumsum(evecs**2, axis=1)**0.5
# If we want k clusters, use the first k normalized eigenvectors.
# Fun exercise: see how the segmentation changes as you vary k
k = 5
X = evecs[:, :k] / Cnorm[:, k-1:k]
# Plot the resulting representation (Figure 1, center and right)
fig, ax = plt.subplots(ncols=2, sharey=True, figsize=(10, 5))
librosa.display.specshow(Rf, cmap='inferno_r', y_axis='time', x_axis='time',
y_coords=beat_times, x_coords=beat_times, ax=ax[1])
ax[1].set(title='Recurrence similarity')
ax[1].label_outer()
librosa.display.specshow(X,
y_axis='time',
y_coords=beat_times, ax=ax[0])
ax[0].set(title='Structure components')
#############################################################
# Let's use these k components to cluster beats into segments
# (Algorithm 1)
KM = sklearn.cluster.KMeans(n_clusters=k)
seg_ids = KM.fit_predict(X)
# and plot the results
fig, ax = plt.subplots(ncols=3, sharey=True, figsize=(10, 4))
colors = plt.get_cmap('Paired', k)
librosa.display.specshow(Rf, cmap='inferno_r', y_axis='time',
y_coords=beat_times, ax=ax[1])
ax[1].set(title='Recurrence matrix')
ax[1].label_outer()
librosa.display.specshow(X,
y_axis='time',
y_coords=beat_times, ax=ax[0])
ax[0].set(title='Structure components')
img = librosa.display.specshow(np.atleast_2d(seg_ids).T, cmap=colors,
y_axis='time', y_coords=beat_times, ax=ax[2])
ax[2].set(title='Estimated segments')
ax[2].label_outer()
fig.colorbar(img, ax=[ax[2]], ticks=range(k))
###############################################################
# Locate segment boundaries from the label sequence
bound_beats = 1 + np.flatnonzero(seg_ids[:-1] != seg_ids[1:])
# Count beat 0 as a boundary
bound_beats = librosa.util.fix_frames(bound_beats, x_min=0)
# Compute the segment label for each boundary
bound_segs = list(seg_ids[bound_beats])
# Convert beat indices to frames
bound_frames = beats[bound_beats]
# Make sure we cover to the end of the track
bound_frames = librosa.util.fix_frames(bound_frames,
x_min=None,
x_max=C.shape[1]-1)
###################################################
# And plot the final segmentation over original CQT
# sphinx_gallery_thumbnail_number = 5
import matplotlib.patches as patches
bound_times = librosa.frames_to_time(bound_frames)
freqs = librosa.cqt_frequencies(n_bins=C.shape[0],
fmin=librosa.note_to_hz('C1'),
bins_per_octave=BINS_PER_OCTAVE)
fig, ax = plt.subplots()
librosa.display.specshow(C, y_axis='cqt_hz', sr=sr,
bins_per_octave=BINS_PER_OCTAVE,
x_axis='time', ax=ax)
for interval, label in zip(zip(bound_times, bound_times[1:]), bound_segs):
ax.add_patch(patches.Rectangle((interval[0], freqs[0]),
interval[1] - interval[0],
freqs[-1],
facecolor=colors(label),
alpha=0.50))
|
bmcfee/librosa
|
docs/examples/plot_segmentation.py
|
Python
|
isc
| 8,172
|
[
"Brian"
] |
a4530b2b1747d39e254603743b8ff712f65f6b48514017c7e06af13019180cf4
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the 'Software'),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
#
################################################################################
"""
Contains classes and functions for working with the various RMG databases. In
particular, this module is devoted to functionality that is common across all
components of the RMG database.
"""
import os
import logging
import re
import codecs
try:
from collections import OrderedDict
except ImportError:
logging.warning("Upgrade to Python 2.7 or later to ensure your database entries are read and written in the same order each time!")
OrderedDict = dict
from rmgpy.molecule import Molecule, Group
from reference import Reference, Article, Book, Thesis
from rmgpy.exceptions import DatabaseError, ForbiddenStructureException, InvalidAdjacencyListError
################################################################################
class Entry(object):
"""
A class for representing individual records in an RMG database. Each entry
in the database associates a chemical item (generally a species, functional
group, or reaction) with a piece of data corresponding to that item. A
significant amount of metadata can also be stored with each entry.
The attributes are:
=================== ========================================================
Attribute Description
=================== ========================================================
`index` A unique nonnegative integer index for the entry
`label` A unique string identifier for the entry (or '' if not used)
`item` The item that this entry represents
`parent` The parent of the entry in the hierarchy (or ``None`` if not used)
`children` A list of the children of the entry in the hierarchy (or ``None`` if not used)
`data` The data to associate with the item
`reference` A :class:`Reference` object containing bibliographic reference information to the source of the data
`referenceType` The way the data was determined: ``'theoretical'``, ``'experimental'``, or ``'review'``
`shortDesc` A brief (one-line) description of the data
`longDesc` A long, verbose description of the data
`rank` An integer indicating the degree of confidence in the entry data, or ``None`` if not used
`nodalDistance` A float representing the distance of a given entry from it's parent entry
=================== ========================================================
"""
def __init__(self,
index=-1,
label='',
item=None,
parent=None,
children=None,
data=None,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
rank=None,
nodalDistance=None,
):
self.index = index
self.label = label
self.item = item
self.parent = parent
self.children = children or []
self.data = data
self.reference = reference
self.referenceType = referenceType
self._shortDesc = unicode(shortDesc)
self._longDesc = unicode(longDesc)
self.rank = rank
self.nodalDistance=nodalDistance
def __str__(self):
return self.label
def __repr__(self):
return '<Entry index={0:d} label="{1}">'.format(self.index, self.label)
@property
def longDesc(self):
return self._longDesc
@longDesc.setter
def longDesc(self, value):
if value is None:
self._longDesc = None
else:
self._longDesc = unicode(value)
@property
def shortDesc(self):
return self._shortDesc
@shortDesc.setter
def shortDesc(self, value):
if value is None:
self._shortDesc = None
else:
self._shortDesc = unicode(value)
################################################################################
class Database:
"""
An RMG-style database, consisting of a dictionary of entries (associating
items with data), and an optional tree for assigning a hierarchy to the
entries. The use of the tree enables the database to be easily extensible
as more parameters are available.
In constructing the tree, it is important to develop a hierarchy such that
siblings are mutually exclusive, to ensure that there is a unique path of
descent down a tree for each structure. If non-mutually exclusive siblings
are encountered, a warning is raised and the parent of the siblings is
returned.
There is no requirement that the children of a node span the range of
more specific permutations of the parent. As the database gets more complex,
attempting to maintain complete sets of children for each parent in each
database rapidly becomes untenable, and is against the spirit of
extensibility behind the database development.
You must derive from this class and implement the :meth:`loadEntry`,
:meth:`saveEntry`, :meth:`processOldLibraryEntry`, and
:meth:`generateOldLibraryEntry` methods in order to load and save from the
new and old database formats.
"""
local_context = {}
local_context['Reference'] = Reference
local_context['Article'] = Article
local_context['Book'] = Book
local_context['Thesis'] = Thesis
def __init__(self,
entries=None,
top=None,
label='',
name='',
solvent=None,
shortDesc='',
longDesc='',
):
self.entries = OrderedDict(entries or {})
self.top = top or []
self.label = label
self.name = name
self.solvent = solvent
self.shortDesc = shortDesc
self.longDesc = longDesc
def load(self, path, local_context=None, global_context=None):
"""
Load an RMG-style database from the file at location `path` on disk.
The parameters `local_context` and `global_context` are used to
provide specialized mapping of identifiers in the input file to
corresponding functions to evaluate. This method will automatically add
a few identifiers required by all data entries, so you don't need to
provide these.
"""
# Collision efficiencies are in SMILES format, so we'll need RDKit
# to convert them to Molecule objects
# Do the import here to ensure it is imported from a pure Python
# environment (as opposed to a Cythonized environment, which is not
# allowed during an exec() call)
from rdkit import Chem
# Clear any previously-loaded data
self.entries = OrderedDict()
self.top = []
# Set up global and local context
if global_context is None: global_context = {}
global_context['__builtins__'] = None
global_context['True'] = True
global_context['False'] = False
if local_context is None: local_context = {}
local_context['__builtins__'] = None
local_context['entry'] = self.loadEntry
local_context['tree'] = self.__loadTree
local_context['name'] = self.name
local_context['solvent'] = self.solvent
local_context['shortDesc'] = self.shortDesc
local_context['longDesc'] = self.longDesc
# add in anything from the Class level dictionary.
for key, value in Database.local_context.iteritems():
local_context[key]=value
# Process the file
f = open(path, 'r')
try:
exec f in global_context, local_context
except Exception:
logging.error('Error while reading database {0!r}.'.format(path))
raise
f.close()
# Extract the database metadata
self.name = local_context['name']
self.solvent = local_context['solvent']
self.shortDesc = local_context['shortDesc']
self.longDesc = local_context['longDesc'].strip()
# Return the loaded database (to allow for Database().load() syntax)
return self
def getEntriesToSave(self):
"""
Return a sorted list of the entries in this database that should be
saved to the output file.
Then renumber the entry indexes so that we never have any duplicate indexes.
"""
entries = self.top[:]
if len(self.top) > 0:
# Save the entries in the same order as the tree (so that it saves
# in the same order each time)
for entry in self.top:
entries.extend(self.descendants(entry))
# It may be that a logical or is defined such that its children
# are not in the tree; this ensures that they still get saved
index = 0
while index < len(entries):
entry = entries[index]
if isinstance(entry.item, LogicOr):
descendants = self.descendants(entry)
for child in entry.item.components:
if self.entries[child] not in descendants:
entries.append(self.entries[child])
index += 1
else:
# Otherwise save the entries sorted by index, if defined
entries = self.entries.values()
entries.sort(key=lambda x: (x.index))
for index, entry in enumerate(entries):
entry.index = index
return entries
def getSpecies(self, path):
"""
Load the dictionary containing all of the species in a kinetics library or depository.
"""
from rmgpy.species import Species
speciesDict = {}
with open(path, 'r') as f:
adjlist = ''
for line in f:
if line.strip() == '' and adjlist.strip() != '':
# Finish this adjacency list
species = Species().fromAdjacencyList(adjlist)
species.generate_resonance_structures()
label = species.label
if label in speciesDict:
raise DatabaseError('Species label "{0}" used for multiple species in {1}.'.format(label, str(self)))
speciesDict[label] = species
adjlist = ''
else:
adjlist += line
else: #reached end of file
if adjlist.strip() != '':
# Finish this adjacency list
species = Species().fromAdjacencyList(adjlist)
species.generate_resonance_structures()
label = species.label
if label in speciesDict:
raise DatabaseError('Species label "{0}" used for multiple species in {1}.'.format(label, str(self)))
speciesDict[label] = species
return speciesDict
def saveDictionary(self, path):
"""
Extract species from all entries associated with a kinetics library or depository and save them
to the path given.
"""
try:
os.makedirs(os.path.dirname(path))
except OSError:
pass
# Extract species from all the entries
speciesDict = {}
entries = self.entries.values()
for entry in entries:
for reactant in entry.item.reactants:
if reactant.label not in speciesDict:
speciesDict[reactant.label] = reactant
for product in entry.item.products:
if product.label not in speciesDict:
speciesDict[product.label] = product
with open(path, 'w') as f:
for label in speciesDict.keys():
f.write(speciesDict[label].molecule[0].toAdjacencyList(label=label, removeH=False))
f.write('\n')
def save(self, path):
"""
Save the current database to the file at location `path` on disk.
"""
try:
os.makedirs(os.path.dirname(path))
except OSError:
pass
entries = self.getEntriesToSave()
f = codecs.open(path, 'w', 'utf-8')
f.write('#!/usr/bin/env python\n')
f.write('# encoding: utf-8\n\n')
f.write('name = "{0}"\n'.format(self.name))
f.write('shortDesc = u"{0}"\n'.format(self.shortDesc))
f.write('longDesc = u"""\n')
f.write(self.longDesc.strip() + '\n')
f.write('"""\n')
for entry in entries:
self.saveEntry(f, entry)
# Write the tree
if len(self.top) > 0:
f.write('tree(\n')
f.write('"""\n')
f.write(self.generateOldTree(self.top, 1))
f.write('"""\n')
f.write(')\n\n')
f.close()
def loadOld(self, dictstr, treestr, libstr, numParameters, numLabels=1, pattern=True):
"""
Load a dictionary-tree-library based database. The database is stored
in three files: `dictstr` is the path to the dictionary, `treestr` to
the tree, and `libstr` to the library. The tree is optional, and should
be set to '' if not desired.
"""
# Load dictionary, library, and (optionally) tree
try:
self.loadOldDictionary(dictstr, pattern)
except Exception, e:
logging.error('Error while reading database {0!r}.'.format(os.path.dirname(dictstr)))
raise
try:
if treestr != '': self.loadOldTree(treestr)
except Exception, e:
logging.error('Error while reading database {0!r}.'.format(os.path.dirname(treestr)))
raise
try:
self.loadOldLibrary(libstr, numParameters, numLabels)
except Exception, e:
logging.error('Error while reading database {0!r}.'.format(os.path.dirname(libstr)))
raise
return self
def loadOldDictionary(self, path, pattern):
"""
Parse an old-style RMG database dictionary located at `path`. An RMG
dictionary is a list of key-value pairs of a one-line string key and a
multi-line string value. Each record is separated by at least one empty
line. Returns a ``dict`` object with the values converted to
:class:`Molecule` or :class:`Group` objects depending on the
value of `pattern`.
"""
# The dictionary being loaded
self.entries = {}
# The current record
record = ''
fdict=None
# Process the dictionary file
try:
fdict = open(path, 'r')
for line in fdict:
line = line.strip()
# If at blank line, end of record has been found
if len(line) == 0 and len(record) > 0:
# Label is first line of record
lines = record.splitlines()
label = lines[0]
# Add record to dictionary
self.entries[label] = Entry(label=label, item=record)
# Clear record in preparation for next iteration
record = ''
# Otherwise append line to record (if not empty and not a comment line)
else:
line = removeCommentFromLine(line).strip()
if len(line) > 0:
record += line + '\n'
# process the last record! (after end of for loop)
# Label is first line of record
if record:
label = record.splitlines()[0]
# Add record to dictionary
self.entries[label] = Entry(label=label, item=record)
except DatabaseError, e:
logging.exception(str(e))
raise
except IOError, e:
logging.exception('Database dictionary file "' + e.filename + '" not found.')
raise
finally:
if fdict: fdict.close()
# Convert the records in the dictionary to Molecule, Group, or
# logical objects
try:
for label in self.entries:
record = self.entries[label].item
lines = record.splitlines()
# If record is a logical node, make it into one.
if re.match("(?i)\s*(NOT\s)?\s*(OR|AND|UNION)\s*(\{.*\})", lines[1]):
self.entries[label].item = makeLogicNode(' '.join(lines[1:]) )
# Otherwise convert adjacency list to molecule or pattern
elif pattern:
self.entries[label].item = Group().fromAdjacencyList(record)
else:
self.entries[label].item = Molecule().fromAdjacencyList(record,saturateH=True)
except InvalidAdjacencyListError, e:
logging.error('Error while loading old-style dictionary "{0}"'.format(path))
logging.error('Error occurred while parsing adjacency list "{0}"'.format(label))
raise
def __loadTree(self, tree):
"""
Parse an group tree located at `tree`. An RMG tree is an n-ary
tree representing the hierarchy of items in the dictionary.
"""
if len(self.entries) == 0:
raise DatabaseError("Load the dictionary before you load the tree.")
# should match ' L3 : foo_bar ' and 'L3:foo_bar'
parser = re.compile('^\s*L(?P<level>\d+)\s*:\s*(?P<label>\S+)')
parents = [None]
for line in tree.splitlines():
line = removeCommentFromLine(line).strip()
if len(line) > 0:
# Extract level
match = parser.match(line)
if not match:
raise DatabaseError("Couldn't parse line '{0}'".format(line.strip()))
level = int(match.group('level'))
label = match.group('label')
# Find immediate parent of the new node
parent = None
if len(parents) < level:
raise DatabaseError("Invalid level specified in line '{0}'".format(line.strip()))
else:
while len(parents) > level:
parents.remove(parents[-1])
if len(parents) > 0:
parent = parents[level-1]
if parent is not None: parent = self.entries[parent]
try:
entry = self.entries[label]
except KeyError:
raise DatabaseError('Unable to find entry "{0}" from tree in dictionary.'.format(label))
if isinstance(parent, str):
raise DatabaseError('Unable to find parent entry "{0}" of entry "{1}" in tree.'.format(parent, label))
# Update the parent and children of the nodes accordingly
if parent is not None:
entry.parent = parent
parent.children.append(entry)
else:
entry.parent = None
self.top.append(entry)
# Save the level of the tree into the entry
entry.level = level
# Add node to list of parents for subsequent iteration
parents.append(label)
def loadOldTree(self, path):
"""
Parse an old-style RMG database tree located at `path`. An RMG
tree is an n-ary tree representing the hierarchy of items in the
dictionary.
"""
tree = []
try:
ftree = open(path, 'r')
tree = ftree.read()
except IOError, e:
logging.exception('Database tree file "' + e.filename + '" not found.')
finally:
ftree.close()
self.__loadTree(tree)
def loadOldLibrary(self, path, numParameters, numLabels=1):
"""
Parse an RMG database library located at `path`.
"""
if len(self.entries) == 0:
raise DatabaseError("Load the dictionary before you load the library.")
entries = self.parseOldLibrary(path, numParameters, numLabels)
# Load the parsed entries into the database, skipping duplicate entries
skippedCount = 0
for index, label, parameters, comment in entries:
if label not in self.entries:
raise DatabaseError('Entry {0!r} in library was not found in dictionary.'.format(label))
if self.entries[label].index != -1:
# The entry is a duplicate, so skip it
logging.debug("There was already something labeled {0} in the {1} library. Ignoring '{2}' ({3})".format(label, self.label, index, parameters))
skippedCount += 1
else:
# The entry is not a duplicate
self.entries[label].index = index
self.entries[label].data = parameters
self.entries[label].shortDesc = comment
if skippedCount > 0:
logging.warning("Skipped {0:d} duplicate entries in {1} library.".format(skippedCount, self.label))
# Make sure each entry with data has a nonnegative index
entries2 = self.entries.values()
entries2.sort(key=lambda entry: entry.index)
index = entries2[-1].index + 1
if index < 1: index = 1
for index0, label, parameters, comment in entries:
if self.entries[label].index < 0:
self.entries[label].index = index
index += 1
def parseOldLibrary(self, path, numParameters, numLabels=1):
"""
Parse an RMG database library located at `path`, returning the loaded
entries (rather than storing them in the database). This method does
not discard duplicate entries.
"""
entries = []
flib = None
try:
flib = codecs.open(path, 'r', 'utf-8', errors='replace')
for line in flib:
line = removeCommentFromLine(line).strip()
if len(line) > 0:
info = line.split()
# Skip if the number of items on the line is invalid
if len(info) < 2:
continue
# Determine if the first item is an index
# This index is optional in the old library format
index = -1
offset = 0
try:
index = int(float(info[0]))
offset = 1
except ValueError:
pass
# Extract label(s)
label = self.__hashLabels(info[offset:offset+numLabels])
offset += numLabels
# Extract numeric parameter(s) or label of node with data to use
if numParameters < 0:
parameters = self.processOldLibraryEntry(info[offset:])
comment = ''
else:
try:
parameters = self.processOldLibraryEntry(info[offset:offset+numParameters])
offset += numParameters
except (IndexError, ValueError), e:
parameters = info[offset]
offset += 1
# Remaining part of string is comment
comment = ' '.join(info[offset:])
comment = comment.strip('"')
entries.append((index, label, parameters, comment))
except DatabaseError, e:
logging.exception(str(e))
logging.exception("path = '{0}'".format(path))
logging.exception("line = '{0}'".format(line))
raise
except IOError, e:
logging.exception('Database library file "' + e.filename + '" not found.')
raise
finally:
if flib: flib.close()
return entries
def saveOld(self, dictstr, treestr, libstr):
"""
Save the current database to a set of text files using the old-style
syntax.
"""
self.saveOldDictionary(dictstr)
if treestr != '':
self.saveOldTree(treestr)
# RMG-Java does not require a frequencies_groups/Library.txt file to
# operate, but errors are raised upon importing to Py if this file is
# not found. This check prevents the placeholder from being discarded.
if 'StatesGroups' not in self.__class__.__name__:
self.saveOldLibrary(libstr)
def saveOldDictionary(self, path):
"""
Save the current database dictionary to a text file using the old-style
syntax.
"""
entries = []
entriesNotInTree = []
# If we have tree information, save the dictionary in the same order as
# the tree (so that it saves in the same order each time)
def getLogicNodeComponents(entry_or_item):
"""
If we want to save an entry, but that is a logic node, we also want
to save its components, recursively. This is a horribly complicated way
to *not* save in the dictionary any things which are not accessed from
(or needed to define things that are accessed from) the tree.
"""
if isinstance(entry_or_item, Entry):
entry = entry_or_item
item = entry.item
nodes = [entry]
else:
entry = None
item = entry_or_item
nodes = []
if isinstance(item, LogicNode):
for child in item.components:
if isinstance(child, LogicNode):
nodes.extend(getLogicNodeComponents(child))
else:
nodes.extend(getLogicNodeComponents(self.entries[child]))
return nodes
else:
return [entry]
if len(self.top) > 0:
for entry in self.top:
entries.extend(getLogicNodeComponents(entry))
for descendant in self.descendants(entry):
for entry2 in getLogicNodeComponents(descendant):
if entry2 not in entries:
entries.append(entry2)
# Don't forget entries that aren't in the tree
for entry in self.entries.values():
if entry not in entries:
entriesNotInTree.append(entry)
entriesNotInTree.sort(key=lambda x: (x.index, x.label))
# Otherwise save the dictionary in any order
else:
# Save the library in order by index
entries = self.entries.values()
entries.sort(key=lambda x: (x.index, x.label))
def comment(s):
"Return the string, with each line prefixed with '// '"
return '\n'.join('// ' + line if line else '' for line in s.split('\n'))
try:
f = open(path, 'w')
f.write('////////////////////////////////////////////////////////////////////////////////\n')
f.write('//\n')
f.write('// {0} dictionary\n'.format(self.name))
f.write('//\n')
f.write('////////////////////////////////////////////////////////////////////////////////\n')
f.write('\n')
for entry in entries:
f.write(entry.label + '\n')
if isinstance(entry.item, Molecule):
try:
f.write(entry.item.toAdjacencyList(removeH=True, oldStyle=True) + '\n')
except InvalidAdjacencyListError:
f.write("// Couldn't save in old syntax adjacency list. Here it is in new syntax:\n")
f.write(comment(entry.item.toAdjacencyList(removeH=False, oldStyle=False) + '\n'))
elif isinstance(entry.item, Group):
f.write(entry.item.toAdjacencyList(oldStyle=True).replace('{2S,2T}', '2') + '\n')
elif isinstance(entry.item, LogicOr):
f.write('{0}\n\n'.format(entry.item).replace('OR{', 'Union {'))
elif entry.label[0:7] == 'Others-':
assert isinstance(entry.item, LogicNode)
f.write('{0}\n\n'.format(entry.item))
else:
raise DatabaseError('Unexpected item with label {0} encountered in dictionary while attempting to save.'.format(entry.label))
if entriesNotInTree:
f.write(comment("These entries do not appear in the tree:\n\n"))
for entry in entriesNotInTree:
f.write(comment(entry.label + '\n'))
if isinstance(entry.item, Molecule):
f.write(comment(entry.item.toAdjacencyList(removeH=False) + '\n'))
elif isinstance(entry.item, Group):
f.write(comment(entry.item.toAdjacencyList().replace('{2S,2T}','2') + '\n'))
elif isinstance(entry.item, LogicOr):
f.write(comment('{0}\n\n'.format(entry.item).replace('OR{', 'Union {')))
elif entry.label[0:7] == 'Others-':
assert isinstance(entry.item, LogicNode)
f.write(comment('{0}\n\n'.format(entry.item)))
else:
raise DatabaseError('Unexpected item with label {0} encountered in dictionary while attempting to save.'.format(entry.label))
f.close()
except IOError, e:
logging.exception('Unable to save old-style dictionary to "{0}".'.format(os.path.abspath(path)))
raise
def generateOldTree(self, entries, level):
"""
Generate a multi-line string representation of the current tree using
the old-style syntax.
"""
string = ''
for entry in entries:
# Write current node
string += '{0}L{1:d}: {2}\n'.format(' ' * (level-1), level, entry.label)
# Recursively descend children (depth-first)
string += self.generateOldTree(entry.children, level+1)
return string
def saveOldTree(self, path):
"""
Save the current database tree to a text file using the old-style
syntax.
"""
try:
f = open(path, 'w')
f.write('////////////////////////////////////////////////////////////////////////////////\n')
f.write('//\n')
f.write('// {0} tree\n'.format(self.name))
f.write('//\n')
f.write('////////////////////////////////////////////////////////////////////////////////\n')
f.write('\n')
f.write(self.generateOldTree(self.top, 1))
f.close()
except IOError, e:
logging.exception('Unable to save old-style tree to "{0}".'.format(os.path.abspath(path)))
raise
def saveOldLibrary(self, path):
"""
Save the current database library to a text file using the old-style
syntax.
"""
try:
# Save the library in order by index
entries = self.entries.values()
entries.sort(key=lambda x: x.index)
f = codecs.open(path, 'w', 'utf-8')
records = []
for entry in entries:
if entry.data is not None:
data = entry.data
if not isinstance(data, str):
data = self.generateOldLibraryEntry(data)
records.append((entry.index, [entry.label], data, entry.shortDesc))
records.sort()
f.write('////////////////////////////////////////////////////////////////////////////////\n')
f.write('//\n')
f.write('// {0} library\n'.format(self.name))
f.write('//\n')
f.write('////////////////////////////////////////////////////////////////////////////////\n')
f.write('\n')
for index, labels, data, comment in records:
f.write('{:<6d} '.format(index))
for label in labels:
f.write('{:<32s} '.format(label))
if isinstance(data, basestring):
f.write('{:s} '.format(data))
else:
f.write('{:s} '.format(' '.join(['{:<10g}'.format(d) for d in data])))
f.write(u' {:s}\n'.format(comment))
f.close()
except IOError, e:
logging.exception('Unable to save old-style library to "{0}".'.format(os.path.abspath(path)))
raise
def __hashLabels(self, labels):
"""
Convert a list of string `labels` to a list of single strings that
represent permutations of the individual strings in the `labels` list::
>>> hashLabels(['a','b'])
['a;b', 'b;a']
"""
return ';'.join(labels)
def ancestors(self, node):
"""
Returns all the ancestors of a node, climbing up the tree to the top.
"""
if isinstance(node, str): node = self.entries[node]
ancestors = []
parent = node.parent
if parent is not None:
ancestors = [parent]
ancestors.extend(self.ancestors(parent))
return ancestors
def descendants(self, node):
"""
Returns all the descendants of a node, climbing down the tree to the bottom.
"""
if isinstance(node, str): node = self.entries[node]
descendants = []
for child in node.children:
descendants.append(child)
descendants.extend(self.descendants(child))
return descendants
def matchNodeToNode(self, node, nodeOther):
"""
Return `True` if `node` and `nodeOther` are identical. Otherwise, return `False`.
Both `node` and `nodeOther` must be Entry types with items containing Group or LogicNode types.
"""
if isinstance(node.item, Group) and isinstance(nodeOther.item, Group):
return self.matchNodeToStructure(node,nodeOther.item, atoms=nodeOther.item.getLabeledAtoms()) and self.matchNodeToStructure(nodeOther,node.item,atoms=node.item.getLabeledAtoms())
elif isinstance(node.item,LogicOr) and isinstance(nodeOther.item,LogicOr):
return node.item.matchLogicOr(nodeOther.item)
else:
# Assume nonmatching
return False
def matchNodeToChild(self, parentNode, childNode):
"""
Return `True` if `parentNode` is a parent of `childNode`. Otherwise, return `False`.
Both `parentNode` and `childNode` must be Entry types with items containing Group or LogicNode types.
If `parentNode` and `childNode` are identical, the function will also return `False`.
"""
if isinstance(parentNode.item, Group) and isinstance(childNode.item, Group):
if self.matchNodeToStructure(parentNode,childNode.item, atoms=childNode.item.getLabeledAtoms(), strict=True) is True:
if self.matchNodeToStructure(childNode,parentNode.item, atoms=parentNode.item.getLabeledAtoms(), strict=True) is False:
return True
return False
#If the parentNode is a Group and the childNode is a LogicOr there is nothing to check,
#except that the parent is listed in the attributes. However, we do need to check that everything down this
#family line is consistent, which is done in the databaseTest unitTest
elif isinstance(parentNode.item, Group) and isinstance(childNode.item, LogicOr):
return childNode.parent is parentNode
elif isinstance(parentNode.item,LogicOr):
return childNode.label in parentNode.item.components
def matchNodeToStructure(self, node, structure, atoms, strict=False):
"""
Return :data:`True` if the `structure` centered at `atom` matches the
structure at `node` in the dictionary. The structure at `node` should
have atoms with the appropriate labels because they are set on loading
and never change. However, the atoms in `structure` may not have the
correct labels, hence the `atoms` parameter. The `atoms` parameter may
include extra labels, and so we only require that every labeled atom in
the functional group represented by `node` has an equivalent labeled
atom in `structure`.
Matching to structure is more strict than to node. All labels in structure must
be found in node. However the reverse is not true, unless `strict` is set to True.
=================== ========================================================
Attribute Description
=================== ========================================================
`node` Either an Entry or a key in the self.entries dictionary which has a Group or LogicNode as its Entry.item
`structure` A Group or a Molecule
`atoms` Dictionary of {label: atom} in the structure. A possible dictionary is the one produced by structure.getLabeledAtoms()
`strict` If set to ``True``, ensures that all the node's atomLabels are matched by in the structure
=================== ========================================================
"""
if isinstance(node, str): node = self.entries[node]
group = node.item
if isinstance(group, LogicNode):
return group.matchToStructure(self, structure, atoms, strict)
else:
# try to pair up labeled atoms
centers = group.getLabeledAtoms()
initialMap = {}
for label in centers.keys():
# Make sure the labels are in both group and structure.
if label not in atoms:
logging.log(0, "Label {0} is in group {1} but not in structure".format(label, node))
if strict:
# structure must match all labeled atoms in node if strict is set to True
return False
continue # with the next label - ring structures might not have all labeled atoms
center = centers[label]
atom = atoms[label]
# Make sure labels actually point to atoms.
if center is None or atom is None:
return False
if isinstance(center, list):
# Currently, no node in the database should have duplicate labels
# The capability to have duplicate labels in Group() exists but does not have any functionality.
raise DatabaseError('Nodes in the database should not have duplicate labels. Node {0} does.'.format(node))
# Semantic check #1: atoms with same label are equivalent
if not atom.isSpecificCaseOf(center):
return False
# Semantic check #2: labeled atoms that share bond in the group (node)
# also share equivalent (or more specific) bond in the structure
for atom2, atom1 in initialMap.iteritems():
if group.hasBond(center, atom1) and structure.hasBond(atom, atom2):
bond1 = group.getBond(center, atom1) # bond1 is group
bond2 = structure.getBond(atom, atom2) # bond2 is structure
if not bond2.isSpecificCaseOf(bond1):
return False
elif group.hasBond(center, atom1): # but structure doesn't
return False
# but we don't mind if...
elif structure.hasBond(atom, atom2): # but group doesn't
logging.debug("We don't mind that structure "+ str(structure) +
" has bond but group {0} doesn't".format(node))
# Passed semantic checks, so add to maps of already-matched atoms
initialMap[atom] = center
# Labeled atoms in the structure that are not in the group should
# not be considered in the isomorphism check, so flag them temporarily
# Without this we would hit a lot of nodes that are ambiguous
flaggedAtoms = [atom for label, atom in structure.getLabeledAtoms().iteritems() if label not in centers]
for atom in flaggedAtoms: atom.ignore = True
# use mapped (labeled) atoms to try to match subgraph
result = structure.isSubgraphIsomorphic(group, initialMap)
# Restore atoms flagged in previous step
for atom in flaggedAtoms: atom.ignore = False
return result
def descendTree(self, structure, atoms, root=None, strict=False):
"""
Descend the tree in search of the functional group node that best
matches the local structure around `atoms` in `structure`.
If root=None then uses the first matching top node.
Returns None if there is no matching root.
Set strict to ``True`` if all labels in final matched node must match that of the
structure. This is used in kinetics groups to find the correct reaction template, but
not generally used in other GAVs due to species generally not being prelabeled.
"""
if root is None:
for root in self.top:
if self.matchNodeToStructure(root, structure, atoms, strict):
break # We've found a matching root
else: # didn't break - matched no top nodes
return None
elif not self.matchNodeToStructure(root, structure, atoms, strict):
return None
next = []
for child in root.children:
if self.matchNodeToStructure(child, structure, atoms, strict):
next.append(child)
if len(next) == 1:
return self.descendTree(structure, atoms, next[0], strict)
elif len(next) == 0:
if len(root.children) > 0 and root.children[-1].label.startswith('Others-'):
return root.children[-1]
else:
return root
else:
#logging.warning('For {0}, a node {1} with overlapping children {2} was encountered in tree with top level nodes {3}. Assuming the first match is the better one.'.format(structure, root, next, self.top))
return self.descendTree(structure, atoms, next[0], strict)
def areSiblings(self, node, nodeOther):
"""
Return `True` if `node` and `nodeOther` have the same parent node. Otherwise, return `False`.
Both `node` and `nodeOther` must be Entry types with items containing Group or LogicNode types.
"""
if node.parent is nodeOther.parent: return True
else: return False
def removeGroup(self, groupToRemove):
"""
Removes a group that is in a tree from the database. In addition to deleting from self.entries,
it must also update the parent/child relationships
Returns the removed group
"""
#Don't remove top nodes or LogicOrs as this will cause lots of problems
if groupToRemove in self.top:
raise Exception("Cannot remove top node: {0} from {1} because it is a top node".format(groupToRemove, self))
elif isinstance(groupToRemove.item, LogicOr):
raise Exception ("Cannot remove top node: {0} from {1} because it is a LogicOr".format(groupToRemove, self))
#Remove from entryToRemove from entries
self.entries.pop(groupToRemove.label)
#If there is a parent, then the group exists in a tree and we should edit relatives
parentR=groupToRemove.parent
if not parentR is None:
#Remove from parent's children attribute
parentR.children.remove(groupToRemove)
#change children's parent attribute to former grandparent
for child in groupToRemove.children:
child.parent = parentR
#extend parent's children attribute with new children
parentR.children.extend(groupToRemove.children)
#A few additional changes needed if parentR is a LogicOr node
if isinstance(parentR.item, LogicOr):
parentR.item.components.remove(groupToRemove.label)
parentR.item.components.extend([child.label for child in groupToRemove.children])
return groupToRemove
class LogicNode:
"""
A base class for AND and OR logic nodes.
"""
symbol="<TBD>" # To be redefined by subclass
def __init__(self,items,invert):
self.components = []
for item in items:
if re.match("(?i)\s*(NOT\s)?\s*(OR|AND|UNION)\s*(\{.*\})",item):
component = makeLogicNode(item)
else:
component = item
self.components.append(component)
self.invert = bool(invert)
def __str__(self):
result = ''
if self.invert: result += 'NOT '
result += self.symbol
result += "{{{0}}}".format(', '.join([str(c) for c in self.components]))
return result
class LogicOr(LogicNode):
"""
A logical OR node. Structure can match any component.
Initialize with a list of component items and a boolean instruction to invert the answer.
"""
symbol = "OR"
def matchToStructure(self,database,structure,atoms,strict=False):
"""
Does this node in the given database match the given structure with the labeled atoms?
Setting `strict` to True makes enforces matching of atomLabels in the structure to every
atomLabel in the node.
"""
for node in self.components:
if isinstance(node,LogicNode):
match = node.matchToStructure(database, structure, atoms, strict)
else:
match = database.matchNodeToStructure(node, structure, atoms, strict)
if match:
return True != self.invert
return False != self.invert
def matchLogicOr(self, other):
"""
Is other the same LogicOr group as self?
"""
if len(self.components)!=len(other.components):
return False
else:
for node in self.components:
if node not in other.components:
return False
return True
def getPossibleStructures(self, entries):
"""
Return a list of the possible structures below this node.
"""
if self.invert: raise NotImplementedError("Finding possible structures of NOT OR nodes not implemented.")
structures = []
for item in self.components:
struct = entries[item].item
if isinstance(struct, LogicNode):
structures.extend(struct.getPossibleStructures(entries))
else:
structures.append(struct)
for struct in structures: # check this worked
assert isinstance(struct,Group)
return structures
class LogicAnd(LogicNode):
"""A logical AND node. Structure must match all components."""
symbol = "AND"
def matchToStructure(self,database,structure,atoms,strict=False):
"""
Does this node in the given database match the given structure with the labeled atoms?
Setting `strict` to True makes enforces matching of atomLabels in the structure to every
atomLabel in the node.
"""
for node in self.components:
if isinstance(node,LogicNode):
match = node.matchToStructure(database, structure, atoms, strict)
else:
match = database.matchNodeToStructure(node, structure, atoms, strict)
if not match:
return False != self.invert
return True != self.invert
def makeLogicNode(string):
"""
Creates and returns a node in the tree which is a logic node.
String should be of the form:
* OR{}
* AND{}
* NOT OR{}
* NOT AND{}
And the returned object will be of class LogicOr or LogicAnd
"""
match = re.match("(?i)\s*(NOT\s)?\s*(OR|AND|UNION)\s*(\{.*\})",string) # the (?i) makes it case-insensitive
if not match:
raise Exception("Unexpected string for Logic Node: {0}".format(string))
if match.group(1): invert = True
else: invert = False
logic = match.group(2) # OR or AND (or Union)
contents = match.group(3).strip()
while contents.startswith('{'):
if not contents.endswith('}'):
raise Exception("Unbalanced braces in Logic Node: {0}".format(string))
contents = contents[1:-1]
items=[]
chars=[]
brace_depth = 0
for character in contents:
if character == '{':
brace_depth += 1
if character == '}':
brace_depth -= 1
if character == ',' and brace_depth == 0:
items.append(''.join(chars).lstrip().rstrip() )
chars = []
else:
chars.append(character)
if chars: # add last item
items.append(''.join(chars).lstrip().rstrip() )
if brace_depth != 0: raise Exception("Unbalanced braces in Logic Node: {0}".format(string))
if logic.upper() in ['OR', 'UNION']:
return LogicOr(items, invert)
if logic == 'AND':
return LogicAnd(items, invert)
raise Exception("Could not create Logic Node from {0}".format(string))
################################################################################
def removeCommentFromLine(line):
"""
Remove a C++/Java style comment from a line of text. This refers
particularly to comments that begin with a double-slash '//' and continue
to the end of the line.
"""
index = line.find('//')
if index >= 0:
line = line[0:index]
return line
def splitLineAndComment(line):
"""
Returns a tuple(line, comment) based on a '//' comment delimiter.
Either `line` or `comment` may be ''.
Does not strip whitespace, nor remove more than two slashes.
"""
split = line.split('//',1)
if len(split) == 1:
return (split[0],'')
else:
return tuple(split)
def getAllCombinations(nodeLists):
"""
Generate a list of all possible combinations of items in the list of
lists `nodeLists`. Each combination takes one item from each list
contained within `nodeLists`. The order of items in the returned lists
reflects the order of lists in `nodeLists`. For example, if `nodeLists` was
[[A, B, C], [N], [X, Y]], the returned combinations would be
[[A, N, X], [A, N, Y], [B, N, X], [B, N, Y], [C, N, X], [C, N, Y]].
"""
items = [[]]
for nodeList in nodeLists:
items = [ item + [node] for node in nodeList for item in items ]
return items
################################################################################
class ForbiddenStructures(Database):
"""
A database consisting solely of structures that are forbidden
from occurring.
"""
def isMoleculeForbidden(self, molecule):
"""
Return ``True`` if the given :class:`Molecule` object `molecule`
contains forbidden functionality, or ``False`` if not. Labeled atoms
on the forbidden structures and the molecule are honored.
"""
for entry in self.entries.values():
entryLabeledAtoms = entry.item.getLabeledAtoms()
moleculeLabeledAtoms = molecule.getLabeledAtoms()
initialMap = {}
for label in entryLabeledAtoms:
# all group labels must be present in the molecule
if label not in moleculeLabeledAtoms: break
initialMap[moleculeLabeledAtoms[label]] = entryLabeledAtoms[label]
else:
if molecule.isMappingValid(entry.item, initialMap) and molecule.isSubgraphIsomorphic(entry.item, initialMap):
return True
# Until we have more thermodynamic data of molecular ions we will forbid them
molecule_charge = 0
for atom in molecule.atoms:
molecule_charge += atom.charge
if molecule_charge != 0:
return True
return False
def loadOld(self, path):
"""
Load an old forbidden structures file from the location `path` on disk.
"""
self.loadOldDictionary(path, pattern=True)
return self
def saveOld(self, path):
"""
Save an old forbidden structures file to the location `path` on disk.
"""
self.saveOldDictionary(path)
def loadEntry(self, label, molecule=None, group=None, shortDesc='', longDesc=''):
"""
Load an entry from the forbidden structures database. This method is
automatically called during loading of the forbidden structures
database.
"""
assert molecule is not None or group is not None
assert not (molecule is not None and group is not None)
if molecule is not None:
item = Molecule.fromAdjacencyList(molecule)
elif group is not None:
if ( group[0:3].upper() == 'OR{' or
group[0:4].upper() == 'AND{' or
group[0:7].upper() == 'NOT OR{' or
group[0:8].upper() == 'NOT AND{'
):
item = makeLogicNode(group)
else:
item = Group().fromAdjacencyList(group)
self.entries[label] = Entry(
label = label,
item = item,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def saveEntry(self, f, entry, name='entry'):
"""
Save an `entry` from the forbidden structures database. This method is
automatically called during saving of the forbidden structures
database.
"""
f.write('{0}(\n'.format(name))
f.write(' label = "{0}",\n'.format(entry.label))
if isinstance(entry.item, Molecule):
f.write(' molecule = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList(removeH=False))
f.write('""",\n')
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
else:
f.write(' group = "{0}",\n'.format(entry.item))
f.write(' shortDesc = u"""{0}""",\n'.format(entry.shortDesc))
f.write(' longDesc = \n')
f.write('u"""\n')
f.write(entry.longDesc.strip() + "\n")
f.write('""",\n')
f.write(')\n\n')
|
Molecular-Image-Recognition/Molecular-Image-Recognition
|
code/rmgpy/data/base.py
|
Python
|
mit
| 57,065
|
[
"RDKit"
] |
f458901395cad966d7de67762691665005b2830c8f9a5c5fec12be16781f722d
|
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','license','copyright','platform','minsdk']
module_defaults = {
'description':'My module',
'author': 'Your Name',
'license' : 'Specify your license',
'copyright' : 'Copyright (c) %s by Your Company' % str(date.today().year),
}
module_license_default = "TODO: place your license here and we'll include it in the module distribution"
def find_sdk(config):
sdk = config['TITANIUM_SDK']
return os.path.expandvars(os.path.expanduser(sdk))
def replace_vars(config,token):
idx = token.find('$(')
while idx != -1:
idx2 = token.find(')',idx+2)
if idx2 == -1: break
key = token[idx+2:idx2]
if not config.has_key(key): break
token = token.replace('$(%s)' % key, config[key])
idx = token.find('$(')
return token
def read_ti_xcconfig():
contents = open(os.path.join(cwd,'titanium.xcconfig')).read()
config = {}
for line in contents.splitlines(False):
line = line.strip()
if line[0:2]=='//': continue
idx = line.find('=')
if idx > 0:
key = line[0:idx].strip()
value = line[idx+1:].strip()
config[key] = replace_vars(config,value)
return config
def generate_doc(config):
docdir = os.path.join(cwd,'documentation')
if not os.path.exists(docdir):
warn("Couldn't find documentation file at: %s" % docdir)
return None
try:
import markdown2 as markdown
except ImportError:
import markdown
documentation = []
for file in os.listdir(docdir):
if file in ignoreFiles or os.path.isdir(os.path.join(docdir, file)):
continue
md = open(os.path.join(docdir,file)).read()
html = markdown.markdown(md)
documentation.append({file:html});
return documentation
def compile_js(manifest,config):
js_file = os.path.join(cwd,'assets','com.testfairy.titestfairy.js')
if not os.path.exists(js_file): return
from compiler import Compiler
try:
import json
except:
import simplejson as json
compiler = Compiler(cwd, manifest['moduleid'], manifest['name'], 'commonjs')
root_asset, module_assets = compiler.compile_module()
root_asset_content = """
%s
return filterDataInRange([NSData dataWithBytesNoCopy:data length:sizeof(data) freeWhenDone:NO], ranges[0]);
""" % root_asset
module_asset_content = """
%s
NSNumber *index = [map objectForKey:path];
if (index == nil) {
return nil;
}
return filterDataInRange([NSData dataWithBytesNoCopy:data length:sizeof(data) freeWhenDone:NO], ranges[index.integerValue]);
""" % module_assets
from tools import splice_code
assets_router = os.path.join(cwd,'Classes','ComTestfairyTitestfairyModuleAssets.m')
splice_code(assets_router, 'asset', root_asset_content)
splice_code(assets_router, 'resolve_asset', module_asset_content)
# Generate the exports after crawling all of the available JS source
exports = open('metadata.json','w')
json.dump({'exports':compiler.exports }, exports)
exports.close()
def die(msg):
print msg
sys.exit(1)
def info(msg):
print "[INFO] %s" % msg
def warn(msg):
print "[WARN] %s" % msg
def validate_license():
c = open(os.path.join(cwd,'LICENSE')).read()
if c.find(module_license_default)!=-1:
warn('please update the LICENSE file with your license text before distributing')
def validate_manifest():
path = os.path.join(cwd,'manifest')
f = open(path)
if not os.path.exists(path): die("missing %s" % path)
manifest = {}
for line in f.readlines():
line = line.strip()
if line[0:1]=='#': continue
if line.find(':') < 0: continue
key,value = line.split(':')
manifest[key.strip()]=value.strip()
for key in required_module_keys:
if not manifest.has_key(key): die("missing required manifest key '%s'" % key)
if module_defaults.has_key(key):
defvalue = module_defaults[key]
curvalue = manifest[key]
if curvalue==defvalue: warn("please update the manifest key: '%s' to a non-default value" % key)
return manifest,path
ignoreFiles = ['.DS_Store','.gitignore','libTitanium.a','titanium.jar','README']
ignoreDirs = ['.DS_Store','.svn','.git','CVSROOT']
def zip_dir(zf,dir,basepath,ignoreExt=[]):
if not os.path.exists(dir): return
for root, dirs, files in os.walk(dir):
for name in ignoreDirs:
if name in dirs:
dirs.remove(name) # don't visit ignored directories
for file in files:
if file in ignoreFiles: continue
e = os.path.splitext(file)
if len(e) == 2 and e[1] in ignoreExt: continue
from_ = os.path.join(root, file)
to_ = from_.replace(dir, '%s/%s'%(basepath,dir), 1)
zf.write(from_, to_)
def glob_libfiles():
files = []
for libfile in glob.glob('build/**/*.a'):
if libfile.find('Release-')!=-1:
files.append(libfile)
return files
def build_module(manifest,config):
from tools import ensure_dev_path
ensure_dev_path()
rc = os.system("xcodebuild -sdk iphoneos -configuration Release")
if rc != 0:
die("xcodebuild failed")
rc = os.system("xcodebuild -sdk iphonesimulator -configuration Release")
if rc != 0:
die("xcodebuild failed")
# build the merged library using lipo
moduleid = manifest['moduleid']
libpaths = ''
for libfile in glob_libfiles():
libpaths+='%s ' % libfile
os.system("lipo %s -create -output build/lib%s.a" %(libpaths,moduleid))
def generate_apidoc(apidoc_build_path):
global options
if options.skip_docs:
info("Skipping documentation generation.")
return False
else:
info("Module apidoc generation can be skipped using --skip-docs")
apidoc_path = os.path.join(cwd, "apidoc")
if not os.path.exists(apidoc_path):
warn("Skipping apidoc generation. No apidoc folder found at: %s" % apidoc_path)
return False
if not os.path.exists(apidoc_build_path):
os.makedirs(apidoc_build_path)
ti_root = string.strip(subprocess.check_output(["echo $TI_ROOT"], shell=True))
if not len(ti_root) > 0:
warn("Not generating documentation from the apidoc folder. The titanium_mobile repo could not be found.")
warn("Set the TI_ROOT environment variable to the parent folder where the titanium_mobile repo resides (eg.'export TI_ROOT=/Path').")
return False
docgen = os.path.join(ti_root, "titanium_mobile", "apidoc", "docgen.py")
if not os.path.exists(docgen):
warn("Not generating documentation from the apidoc folder. Couldn't find docgen.py at: %s" % docgen)
return False
info("Generating documentation from the apidoc folder.")
rc = os.system("\"%s\" --format=jsca,modulehtml --css=styles.css -o \"%s\" -e \"%s\"" % (docgen, apidoc_build_path, apidoc_path))
if rc != 0:
die("docgen failed")
return True
def package_module(manifest,mf,config):
name = manifest['name'].lower()
moduleid = manifest['moduleid'].lower()
version = manifest['version']
modulezip = '%s-iphone-%s.zip' % (moduleid,version)
if os.path.exists(modulezip): os.remove(modulezip)
zf = zipfile.ZipFile(modulezip, 'w', zipfile.ZIP_DEFLATED)
modulepath = 'modules/iphone/%s/%s' % (moduleid,version)
zf.write(mf,'%s/manifest' % modulepath)
libname = 'lib%s.a' % moduleid
zf.write('build/%s' % libname, '%s/%s' % (modulepath,libname))
docs = generate_doc(config)
if docs!=None:
for doc in docs:
for file, html in doc.iteritems():
filename = string.replace(file,'.md','.html')
zf.writestr('%s/documentation/%s'%(modulepath,filename),html)
apidoc_build_path = os.path.join(cwd, "build", "apidoc")
if generate_apidoc(apidoc_build_path):
for file in os.listdir(apidoc_build_path):
if file in ignoreFiles or os.path.isdir(os.path.join(apidoc_build_path, file)):
continue
zf.write(os.path.join(apidoc_build_path, file), '%s/documentation/apidoc/%s' % (modulepath, file))
zip_dir(zf,'assets',modulepath,['.pyc','.js'])
zip_dir(zf,'example',modulepath,['.pyc'])
zip_dir(zf,'platform',modulepath,['.pyc','.js'])
zf.write('LICENSE','%s/LICENSE' % modulepath)
zf.write('module.xcconfig','%s/module.xcconfig' % modulepath)
exports_file = 'metadata.json'
if os.path.exists(exports_file):
zf.write(exports_file, '%s/%s' % (modulepath, exports_file))
zf.close()
if __name__ == '__main__':
global options
parser = optparse.OptionParser()
parser.add_option("-s", "--skip-docs",
dest="skip_docs",
action="store_true",
help="Will skip building documentation in apidoc folder",
default=False)
(options, args) = parser.parse_args()
manifest,mf = validate_manifest()
validate_license()
config = read_ti_xcconfig()
sdk = find_sdk(config)
sys.path.insert(0,os.path.join(sdk,'iphone'))
sys.path.append(os.path.join(sdk, "common"))
compile_js(manifest,config)
build_module(manifest,config)
package_module(manifest,mf,config)
sys.exit(0)
|
titanium-forks/testfairy.ti.testfairy
|
build.py
|
Python
|
apache-2.0
| 8,789
|
[
"VisIt"
] |
10bda057c491378583833d6a7c77f15c495bd2c3f362512b9bd35a90c46e7714
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative sampling [1]_ [2]_.
The training algorithms were originally ported from the C package https://code.google.com/p/word2vec/
and extended with additional functionality.
For a blog tutorial on gensim word2vec, with an interactive web app trained on GoogleNews, visit http://radimrehurek.com/2014/02/word2vec-tutorial/
**Make sure you have a C compiler before installing gensim, to use optimized (compiled) word2vec training**
(70x speedup compared to plain NumPy implementation [3]_).
Initialize a model with e.g.::
>>> model = Word2Vec(sentences, size=100, window=5, min_count=5, workers=4)
Persist a model to disk with::
>>> model.save(fname)
>>> model = Word2Vec.load(fname) # you can continue training with the loaded model!
The model can also be instantiated from an existing file on disk in the word2vec C format::
>>> model = Word2Vec.load_word2vec_format('/tmp/vectors.txt', binary=False) # C text format
>>> model = Word2Vec.load_word2vec_format('/tmp/vectors.bin', binary=True) # C binary format
You can perform various syntactic/semantic NLP word tasks with the model. Some of them
are already built-in::
>>> model.most_similar(positive=['woman', 'king'], negative=['man'])
[('queen', 0.50882536), ...]
>>> model.doesnt_match("breakfast cereal dinner lunch".split())
'cereal'
>>> model.similarity('woman', 'man')
0.73723527
>>> model['computer'] # raw numpy vector of a word
array([-0.00449447, -0.00310097, 0.02421786, ...], dtype=float32)
and so on.
If you're finished training a model (=no more updates, only querying), you can do
>>> model.init_sims(replace=True)
to trim unneeded model memory = use (much) less RAM.
Note that there is a :mod:`gensim.models.phrases` module which lets you automatically
detect phrases longer than one word. Using phrases, you can learn a word2vec model
where "words" are actually multiword expressions, such as `new_york_times` or `financial_crisis`:
>>> bigram_transformer = gensim.models.Phrases(sentences)
>>> model = Word2Vec(bigram_transformer[sentences], size=100, ...)
.. [1] Tomas Mikolov, Kai Chen, Greg Corrado, and Jeffrey Dean. Efficient Estimation of Word Representations in Vector Space. In Proceedings of Workshop at ICLR, 2013.
.. [2] Tomas Mikolov, Ilya Sutskever, Kai Chen, Greg Corrado, and Jeffrey Dean. Distributed Representations of Words and Phrases and their Compositionality.
In Proceedings of NIPS, 2013.
.. [3] Optimizing word2vec in gensim, http://radimrehurek.com/2013/09/word2vec-in-python-part-two-optimizing/
"""
from __future__ import division # py3 "true division"
import logging
import sys
import os
import heapq
from timeit import default_timer
from copy import deepcopy
from collections import defaultdict
import threading
import itertools
from gensim.utils import keep_vocab_item
try:
from queue import Queue, Empty
except ImportError:
from Queue import Queue, Empty
from numpy import exp, log, dot, zeros, outer, random, dtype, float32 as REAL,\
uint32, seterr, array, uint8, vstack, fromstring, sqrt, newaxis,\
ndarray, empty, sum as np_sum, prod, ones, ascontiguousarray
from gensim import utils, matutils # utility fnc for pickling, common scipy operations etc
from six import iteritems, itervalues, string_types
from six.moves import xrange
from types import GeneratorType
logger = logging.getLogger(__name__)
try:
from gensim.models.word2vec_inner import train_batch_sg, train_batch_cbow
from gensim.models.word2vec_inner import score_sentence_sg, score_sentence_cbow
from gensim.models.word2vec_inner import FAST_VERSION, MAX_WORDS_IN_BATCH
except ImportError:
# failed... fall back to plain numpy (20-80x slower training than the above)
FAST_VERSION = -1
MAX_WORDS_IN_BATCH = 10000
def train_batch_sg(model, sentences, alpha, work=None):
"""
Update skip-gram model by training on a sequence of sentences.
Each sentence is a list of string tokens, which are looked up in the model's
vocab dictionary. Called internally from `Word2Vec.train()`.
This is the non-optimized, Python version. If you have cython installed, gensim
will use the optimized version from word2vec_inner instead.
"""
result = 0
for sentence in sentences:
word_vocabs = [model.vocab[w] for w in sentence if w in model.vocab and
model.vocab[w].sample_int > model.random.rand() * 2**32]
for pos, word in enumerate(word_vocabs):
reduced_window = model.random.randint(model.window) # `b` in the original word2vec code
# now go over all words from the (reduced) window, predicting each one in turn
start = max(0, pos - model.window + reduced_window)
for pos2, word2 in enumerate(word_vocabs[start:(pos + model.window + 1 - reduced_window)], start):
# don't train on the `word` itself
if pos2 != pos:
train_sg_pair(model, model.index2word[word.index], word2.index, alpha)
result += len(word_vocabs)
return result
def train_batch_cbow(model, sentences, alpha, work=None, neu1=None):
"""
Update CBOW model by training on a sequence of sentences.
Each sentence is a list of string tokens, which are looked up in the model's
vocab dictionary. Called internally from `Word2Vec.train()`.
This is the non-optimized, Python version. If you have cython installed, gensim
will use the optimized version from word2vec_inner instead.
"""
result = 0
for sentence in sentences:
word_vocabs = [model.vocab[w] for w in sentence if w in model.vocab and
model.vocab[w].sample_int > model.random.rand() * 2**32]
for pos, word in enumerate(word_vocabs):
reduced_window = model.random.randint(model.window) # `b` in the original word2vec code
start = max(0, pos - model.window + reduced_window)
window_pos = enumerate(word_vocabs[start:(pos + model.window + 1 - reduced_window)], start)
word2_indices = [word2.index for pos2, word2 in window_pos if (word2 is not None and pos2 != pos)]
l1 = np_sum(model.syn0[word2_indices], axis=0) # 1 x vector_size
if word2_indices and model.cbow_mean:
l1 /= len(word2_indices)
train_cbow_pair(model, word, word2_indices, l1, alpha)
result += len(word_vocabs)
return result
def score_sentence_sg(model, sentence, work=None):
"""
Obtain likelihood score for a single sentence in a fitted skip-gram representaion.
The sentence is a list of Vocab objects (or None, when the corresponding
word is not in the vocabulary). Called internally from `Word2Vec.score()`.
This is the non-optimized, Python version. If you have cython installed, gensim
will use the optimized version from word2vec_inner instead.
"""
log_prob_sentence = 0.0
if model.negative:
raise RuntimeError("scoring is only available for HS=True")
word_vocabs = [model.vocab[w] for w in sentence if w in model.vocab]
for pos, word in enumerate(word_vocabs):
if word is None:
continue # OOV word in the input sentence => skip
# now go over all words from the window, predicting each one in turn
start = max(0, pos - model.window)
for pos2, word2 in enumerate(word_vocabs[start : pos + model.window + 1], start):
# don't train on OOV words and on the `word` itself
if word2 is not None and pos2 != pos:
log_prob_sentence += score_sg_pair(model, word, word2)
return log_prob_sentence
def score_sentence_cbow(model, sentence, alpha, work=None, neu1=None):
"""
Obtain likelihood score for a single sentence in a fitted CBOW representaion.
The sentence is a list of Vocab objects (or None, where the corresponding
word is not in the vocabulary. Called internally from `Word2Vec.score()`.
This is the non-optimized, Python version. If you have cython installed, gensim
will use the optimized version from word2vec_inner instead.
"""
log_prob_sentence = 0.0
if model.negative:
raise RuntimeError("scoring is only available for HS=True")
word_vocabs = [model.vocab[w] for w in sentence if w in model.vocab]
for pos, word in enumerate(word_vocabs):
if word is None:
continue # OOV word in the input sentence => skip
start = max(0, pos - model.window)
window_pos = enumerate(word_vocabs[start:(pos + model.window + 1)], start)
word2_indices = [word2.index for pos2, word2 in window_pos if (word2 is not None and pos2 != pos)]
l1 = np_sum(model.syn0[word2_indices], axis=0) # 1 x layer1_size
if word2_indices and model.cbow_mean:
l1 /= len(word2_indices)
log_prob_sentence += score_cbow_pair(model, word, word2_indices, l1)
return log_prob_sentence
def train_sg_pair(model, word, context_index, alpha, learn_vectors=True, learn_hidden=True,
context_vectors=None, context_locks=None):
if context_vectors is None:
context_vectors = model.syn0
if context_locks is None:
context_locks = model.syn0_lockf
if word not in model.vocab:
return
predict_word = model.vocab[word] # target word (NN output)
l1 = context_vectors[context_index] # input word (NN input/projection layer)
lock_factor = context_locks[context_index]
neu1e = zeros(l1.shape)
if model.hs:
# work on the entire tree at once, to push as much work into numpy's C routines as possible (performance)
l2a = deepcopy(model.syn1[predict_word.point]) # 2d matrix, codelen x layer1_size
fa = 1.0 / (1.0 + exp(-dot(l1, l2a.T))) # propagate hidden -> output
ga = (1 - predict_word.code - fa) * alpha # vector of error gradients multiplied by the learning rate
if learn_hidden:
model.syn1[predict_word.point] += outer(ga, l1) # learn hidden -> output
neu1e += dot(ga, l2a) # save error
if model.negative:
# use this word (label = 1) + `negative` other random words not from this sentence (label = 0)
word_indices = [predict_word.index]
while len(word_indices) < model.negative + 1:
w = model.cum_table.searchsorted(model.random.randint(model.cum_table[-1]))
if w != predict_word.index:
word_indices.append(w)
l2b = model.syn1neg[word_indices] # 2d matrix, k+1 x layer1_size
fb = 1. / (1. + exp(-dot(l1, l2b.T))) # propagate hidden -> output
gb = (model.neg_labels - fb) * alpha # vector of error gradients multiplied by the learning rate
if learn_hidden:
model.syn1neg[word_indices] += outer(gb, l1) # learn hidden -> output
neu1e += dot(gb, l2b) # save error
if learn_vectors:
l1 += neu1e * lock_factor # learn input -> hidden (mutates model.syn0[word2.index], if that is l1)
return neu1e
def train_cbow_pair(model, word, input_word_indices, l1, alpha, learn_vectors=True, learn_hidden=True):
neu1e = zeros(l1.shape)
if model.hs:
l2a = model.syn1[word.point] # 2d matrix, codelen x layer1_size
fa = 1. / (1. + exp(-dot(l1, l2a.T))) # propagate hidden -> output
ga = (1. - word.code - fa) * alpha # vector of error gradients multiplied by the learning rate
if learn_hidden:
model.syn1[word.point] += outer(ga, l1) # learn hidden -> output
neu1e += dot(ga, l2a) # save error
if model.negative:
# use this word (label = 1) + `negative` other random words not from this sentence (label = 0)
word_indices = [word.index]
while len(word_indices) < model.negative + 1:
w = model.cum_table.searchsorted(model.random.randint(model.cum_table[-1]))
if w != word.index:
word_indices.append(w)
l2b = model.syn1neg[word_indices] # 2d matrix, k+1 x layer1_size
fb = 1. / (1. + exp(-dot(l1, l2b.T))) # propagate hidden -> output
gb = (model.neg_labels - fb) * alpha # vector of error gradients multiplied by the learning rate
if learn_hidden:
model.syn1neg[word_indices] += outer(gb, l1) # learn hidden -> output
neu1e += dot(gb, l2b) # save error
if learn_vectors:
# learn input -> hidden, here for all words in the window separately
if not model.cbow_mean and input_word_indices:
neu1e /= len(input_word_indices)
for i in input_word_indices:
model.syn0[i] += neu1e * model.syn0_lockf[i]
return neu1e
def score_sg_pair(model, word, word2):
l1 = model.syn0[word2.index]
l2a = deepcopy(model.syn1[word.point]) # 2d matrix, codelen x layer1_size
sgn = -1.0**word.code # ch function, 0-> 1, 1 -> -1
lprob = -log(1.0 + exp(-sgn*dot(l1, l2a.T)))
return sum(lprob)
def score_cbow_pair(model, word, word2_indices, l1):
l2a = model.syn1[word.point] # 2d matrix, codelen x layer1_size
sgn = -1.0**word.code # ch function, 0-> 1, 1 -> -1
lprob = -log(1.0 + exp(-sgn*dot(l1, l2a.T)))
return sum(lprob)
class Vocab(object):
"""
A single vocabulary item, used internally for collecting per-word frequency/sampling info,
and for constructing binary trees (incl. both word leaves and inner nodes).
"""
def __init__(self, **kwargs):
self.count = 0
self.__dict__.update(kwargs)
def __lt__(self, other): # used for sorting in a priority queue
return self.count < other.count
def __str__(self):
vals = ['%s:%r' % (key, self.__dict__[key]) for key in sorted(self.__dict__) if not key.startswith('_')]
return "%s(%s)" % (self.__class__.__name__, ', '.join(vals))
class Word2Vec(utils.SaveLoad):
"""
Class for training, using and evaluating neural networks described in https://code.google.com/p/word2vec/
The model can be stored/loaded via its `save()` and `load()` methods, or stored/loaded in a format
compatible with the original word2vec implementation via `save_word2vec_format()` and `load_word2vec_format()`.
"""
def __init__(
self, sentences=None, size=100, alpha=0.025, window=5, min_count=5,
max_vocab_size=None, sample=1e-3, seed=1, workers=3, min_alpha=0.0001,
sg=0, hs=0, negative=5, cbow_mean=1, hashfxn=hash, iter=5, null_word=0,
trim_rule=None, sorted_vocab=1, batch_words=MAX_WORDS_IN_BATCH):
"""
Initialize the model from an iterable of `sentences`. Each sentence is a
list of words (unicode strings) that will be used for training.
The `sentences` iterable can be simply a list, but for larger corpora,
consider an iterable that streams the sentences directly from disk/network.
See :class:`BrownCorpus`, :class:`Text8Corpus` or :class:`LineSentence` in
this module for such examples.
If you don't supply `sentences`, the model is left uninitialized -- use if
you plan to initialize it in some other way.
`sg` defines the training algorithm. By default (`sg=0`), CBOW is used.
Otherwise (`sg=1`), skip-gram is employed.
`size` is the dimensionality of the feature vectors.
`window` is the maximum distance between the current and predicted word within a sentence.
`alpha` is the initial learning rate (will linearly drop to zero as training progresses).
`seed` = for the random number generator. Initial vectors for each
word are seeded with a hash of the concatenation of word + str(seed).
`min_count` = ignore all words with total frequency lower than this.
`max_vocab_size` = limit RAM during vocabulary building; if there are more unique
words than this, then prune the infrequent ones. Every 10 million word types
need about 1GB of RAM. Set to `None` for no limit (default).
`sample` = threshold for configuring which higher-frequency words are randomly downsampled;
default is 1e-3, useful range is (0, 1e-5).
`workers` = use this many worker threads to train the model (=faster training with multicore machines).
`hs` = if 1, hierarchical softmax will be used for model training.
If set to 0 (default), and `negative` is non-zero, negative sampling will be used.
`negative` = if > 0, negative sampling will be used, the int for negative
specifies how many "noise words" should be drawn (usually between 5-20).
Default is 5. If set to 0, no negative samping is used.
`cbow_mean` = if 0, use the sum of the context word vectors. If 1 (default), use the mean.
Only applies when cbow is used.
`hashfxn` = hash function to use to randomly initialize weights, for increased
training reproducibility. Default is Python's rudimentary built in hash function.
`iter` = number of iterations (epochs) over the corpus.
`trim_rule` = vocabulary trimming rule, specifies whether certain words should remain
in the vocabulary, be trimmed away, or handled using the default (discard if word count < min_count).
Can be None (min_count will be used), or a callable that accepts parameters (word, count, min_count) and
returns either util.RULE_DISCARD, util.RULE_KEEP or util.RULE_DEFAULT.
Note: The rule, if given, is only used prune vocabulary during build_vocab() and is not stored as part
of the model.
`sorted_vocab` = if 1 (default), sort the vocabulary by descending frequency before
assigning word indexes.
`batch_words` = target size (in words) for batches of examples passed to worker threads (and
thus cython routines). Default is 10000. (Larger batches can be passed if individual
texts are longer, but the cython code may truncate.)
"""
self.vocab = {} # mapping from a word (string) to a Vocab object
self.index2word = [] # map from a word's matrix index (int) to word (string)
self.sg = int(sg)
self.cum_table = None # for negative sampling
self.vector_size = int(size)
self.layer1_size = int(size)
if size % 4 != 0:
logger.warning("consider setting layer size to a multiple of 4 for greater performance")
self.alpha = float(alpha)
self.window = int(window)
self.max_vocab_size = max_vocab_size
self.seed = seed
self.random = random.RandomState(seed)
self.min_count = min_count
self.sample = sample
self.workers = int(workers)
self.min_alpha = float(min_alpha)
self.hs = hs
self.negative = negative
self.cbow_mean = int(cbow_mean)
self.hashfxn = hashfxn
self.iter = iter
self.null_word = null_word
self.train_count = 0
self.total_train_time = 0
self.sorted_vocab = sorted_vocab
self.batch_words = batch_words
if sentences is not None:
if isinstance(sentences, GeneratorType):
raise TypeError("You can't pass a generator as the sentences argument. Try an iterator.")
self.build_vocab(sentences, trim_rule=trim_rule)
self.train(sentences)
def make_cum_table(self, power=0.75, domain=2**31 - 1):
"""
Create a cumulative-distribution table using stored vocabulary word counts for
drawing random words in the negative-sampling training routines.
To draw a word index, choose a random integer up to the maximum value in the
table (cum_table[-1]), then finding that integer's sorted insertion point
(as if by bisect_left or ndarray.searchsorted()). That insertion point is the
drawn index, coming up in proportion equal to the increment at that slot.
Called internally from 'build_vocab()'.
"""
vocab_size = len(self.index2word)
self.cum_table = zeros(vocab_size, dtype=uint32)
# compute sum of all power (Z in paper)
train_words_pow = float(sum([self.vocab[word].count**power for word in self.vocab]))
cumulative = 0.0
for word_index in range(vocab_size):
cumulative += self.vocab[self.index2word[word_index]].count**power / train_words_pow
self.cum_table[word_index] = round(cumulative * domain)
if len(self.cum_table) > 0:
assert self.cum_table[-1] == domain
def create_binary_tree(self):
"""
Create a binary Huffman tree using stored vocabulary word counts. Frequent words
will have shorter binary codes. Called internally from `build_vocab()`.
"""
logger.info("constructing a huffman tree from %i words", len(self.vocab))
# build the huffman tree
heap = list(itervalues(self.vocab))
heapq.heapify(heap)
for i in xrange(len(self.vocab) - 1):
min1, min2 = heapq.heappop(heap), heapq.heappop(heap)
heapq.heappush(heap, Vocab(count=min1.count + min2.count, index=i + len(self.vocab), left=min1, right=min2))
# recurse over the tree, assigning a binary code to each vocabulary word
if heap:
max_depth, stack = 0, [(heap[0], [], [])]
while stack:
node, codes, points = stack.pop()
if node.index < len(self.vocab):
# leaf node => store its path from the root
node.code, node.point = codes, points
max_depth = max(len(codes), max_depth)
else:
# inner node => continue recursion
points = array(list(points) + [node.index - len(self.vocab)], dtype=uint32)
stack.append((node.left, array(list(codes) + [0], dtype=uint8), points))
stack.append((node.right, array(list(codes) + [1], dtype=uint8), points))
logger.info("built huffman tree with maximum node depth %i", max_depth)
def build_vocab(self, sentences, keep_raw_vocab=False, trim_rule=None, update=False):
"""
Build vocabulary from a sequence of sentences (can be a once-only generator stream).
Each sentence must be a list of unicode strings.
"""
self.scan_vocab(sentences, update, trim_rule=trim_rule) # initial survey
self.scale_vocab(update, keep_raw_vocab=keep_raw_vocab, trim_rule=trim_rule) # trim by min_count & precalculate downsampling
self.finalize_vocab(update) # build tables & arrays
def scan_vocab(self, sentences, update, progress_per=10000, trim_rule=None):
"""Do an initial scan of all words appearing in sentences."""
logger.info("collecting all words and their counts")
sentence_no = -1
total_words = 0
min_reduce = 1
vocab = defaultdict(int)
for sentence_no, sentence in enumerate(sentences):
if sentence_no % progress_per == 0:
logger.info("PROGRESS: at sentence #%i, processed %i words, keeping %i word types",
sentence_no, sum(itervalues(vocab)) + total_words, len(vocab))
for word in sentence:
vocab[word] += 1
if not update:
if self.max_vocab_size and len(vocab) > self.max_vocab_size:
total_words += utils.prune_vocab(vocab, min_reduce, trim_rule=trim_rule)
min_reduce += 1
total_words += sum(itervalues(vocab))
logger.info("collected %i word types from a corpus of %i raw words and %i sentences",
len(vocab), total_words, sentence_no + 1)
self.corpus_count = sentence_no + 1
self.raw_vocab = vocab
def scale_vocab(self, update, min_count=None, sample=None, dry_run=False, keep_raw_vocab=False, trim_rule=None):
"""
Apply vocabulary settings for `min_count` (discarding less-frequent words)
and `sample` (controlling the downsampling of more-frequent words).
Calling with `dry_run=True` will only simulate the provided settings and
report the size of the retained vocabulary, effective corpus length, and
estimated memory requirements. Results are both printed via logging and
returned as a dict.
Delete the raw vocabulary after the scaling is done to free up RAM,
unless `keep_raw_vocab` is set.
"""
min_count = min_count or self.min_count
sample = sample or self.sample
drop_unique, drop_total, retain_total, original_total = 0, 0, 0, 0
retain_words = []
if not update:
logger.info("Loading a fresh vocabulary")
# Discard words less-frequent than min_count
if not dry_run:
self.index2word = []
# make stored settings match these applied settings
self.min_count = min_count
self.sample = sample
self.vocab = {}
for word, v in iteritems(self.raw_vocab):
if keep_vocab_item(word, v, min_count, trim_rule=trim_rule):
retain_words.append(word)
retain_total += v
original_total += v
if not dry_run:
self.vocab[word] = Vocab(count=v,
index=len(self.index2word))
self.index2word.append(word)
else:
drop_unique += 1
drop_total += v
original_total += v
else:
logger.info("Updating model with new vocabulary")
for word, v in iteritems(self.raw_vocab):
if not word in self.vocab:
# the word does not already exist in vocab
if keep_vocab_item(word, v, min_count,
trim_rule=trim_rule):
retain_words.append(word)
retain_total += v
original_total += v
if not dry_run:
self.vocab[word] = Vocab(count=v,
index=len(self.index2word))
self.index2word.append(word)
else:
drop_unique += 1
drop_total += v
original_total += v
logger.info("min_count=%d retains %i unique words (drops %i)",
min_count, len(retain_words), drop_unique)
logger.info("min_count leaves %i word corpus (%i%% of original %i)",
retain_total, retain_total * 100 / max(original_total, 1), original_total)
# Precalculate each vocabulary item's threshold for sampling
if not sample:
# no words downsampled
threshold_count = retain_total
elif sample < 1.0:
# traditional meaning: set parameter as proportion of total
threshold_count = sample * retain_total
else:
# new shorthand: sample >= 1 means downsample all words with higher count than sample
threshold_count = int(sample * (3 + sqrt(5)) / 2)
downsample_total, downsample_unique = 0, 0
for w in retain_words:
v = self.raw_vocab[w]
word_probability = (sqrt(v / threshold_count) + 1) * (threshold_count / v)
if word_probability < 1.0:
downsample_unique += 1
downsample_total += word_probability * v
else:
word_probability = 1.0
downsample_total += v
if not dry_run:
self.vocab[w].sample_int = int(round(word_probability * 2**32))
if not dry_run and not keep_raw_vocab:
logger.info("deleting the raw counts dictionary of %i items", len(self.raw_vocab))
self.raw_vocab = defaultdict(int)
logger.info("sample=%g downsamples %i most-common words", sample, downsample_unique)
logger.info("downsampling leaves estimated %i word corpus (%.1f%% of prior %i)",
downsample_total, downsample_total * 100.0 / max(retain_total, 1), retain_total)
# return from each step: words-affected, resulting-corpus-size
report_values = {'drop_unique': drop_unique, 'retain_total': retain_total,
'downsample_unique': downsample_unique, 'downsample_total': int(downsample_total)}
# print extra memory estimates
report_values['memory'] = self.estimate_memory(vocab_size=len(retain_words))
return report_values
def finalize_vocab(self, update):
"""Build tables and model weights based on final vocabulary settings."""
if not self.index2word:
self.scale_vocab(False)
if self.sorted_vocab and not update:
self.sort_vocab()
if self.hs:
# add info about each word's Huffman encoding
self.create_binary_tree()
if self.negative:
# build the table for drawing random words (for negative sampling)
self.make_cum_table()
if self.null_word:
# create null pseudo-word for padding when using concatenative L1 (run-of-words)
# this word is only ever input – never predicted – so count, huffman-point, etc doesn't matter
word, v = '\0', Vocab(count=1, sample_int=0)
v.index = len(self.vocab)
self.index2word.append(word)
self.vocab[word] = v
# set initial input/projection and hidden weights
if not update:
self.reset_weights()
else:
self.update_weights()
def sort_vocab(self):
"""Sort the vocabulary so the most frequent words have the lowest indexes."""
if hasattr(self, 'syn0'):
raise RuntimeError("must sort before initializing vectors/weights")
self.index2word.sort(key=lambda word: self.vocab[word].count, reverse=True)
for i, word in enumerate(self.index2word):
self.vocab[word].index = i
def reset_from(self, other_model):
"""
Borrow shareable pre-built structures (like vocab) from the other_model. Useful
if testing multiple models in parallel on the same corpus.
"""
self.vocab = other_model.vocab
self.index2word = other_model.index2word
self.cum_table = other_model.cum_table
self.corpus_count = other_model.corpus_count
self.reset_weights()
def _do_train_job(self, sentences, alpha, inits):
"""
Train a single batch of sentences. Return 2-tuple `(effective word count after
ignoring unknown words and sentence length trimming, total word count)`.
"""
work, neu1 = inits
tally = 0
if self.sg:
tally += train_batch_sg(self, sentences, alpha, work)
else:
tally += train_batch_cbow(self, sentences, alpha, work, neu1)
return tally, self._raw_word_count(sentences)
def _raw_word_count(self, job):
"""Return the number of words in a given job."""
return sum(len(sentence) for sentence in job)
def train(self, sentences, total_words=None, word_count=0,
total_examples=None, queue_factor=2, report_delay=1.0):
"""
Update the model's neural weights from a sequence of sentences (can be a once-only generator stream).
For Word2Vec, each sentence must be a list of unicode strings. (Subclasses may accept other examples.)
To support linear learning-rate decay from (initial) alpha to min_alpha, either total_examples
(count of sentences) or total_words (count of raw words in sentences) should be provided, unless the
sentences are the same as those that were used to initially build the vocabulary.
"""
if FAST_VERSION < 0:
import warnings
warnings.warn("C extension not loaded for Word2Vec, training will be slow. "
"Install a C compiler and reinstall gensim for fast training.")
self.neg_labels = []
if self.negative > 0:
# precompute negative labels optimization for pure-python training
self.neg_labels = zeros(self.negative + 1)
self.neg_labels[0] = 1.
logger.info(
"training model with %i workers on %i vocabulary and %i features, "
"using sg=%s hs=%s sample=%s negative=%s",
self.workers, len(self.vocab), self.layer1_size, self.sg,
self.hs, self.sample, self.negative)
if not self.vocab:
raise RuntimeError("you must first build vocabulary before training the model")
if not hasattr(self, 'syn0'):
raise RuntimeError("you must first finalize vocabulary before training the model")
if total_words is None and total_examples is None:
if self.corpus_count:
total_examples = self.corpus_count
logger.info("expecting %i sentences, matching count from corpus used for vocabulary survey", total_examples)
else:
raise ValueError("you must provide either total_words or total_examples, to enable alpha and progress calculations")
job_tally = 0
if self.iter > 1:
sentences = utils.RepeatCorpusNTimes(sentences, self.iter)
total_words = total_words and total_words * self.iter
total_examples = total_examples and total_examples * self.iter
def worker_loop():
"""Train the model, lifting lists of sentences from the job_queue."""
work = matutils.zeros_aligned(self.layer1_size, dtype=REAL) # per-thread private work memory
neu1 = matutils.zeros_aligned(self.layer1_size, dtype=REAL)
jobs_processed = 0
while True:
job = job_queue.get()
if job is None:
progress_queue.put(None)
break # no more jobs => quit this worker
sentences, alpha = job
tally, raw_tally = self._do_train_job(sentences, alpha, (work, neu1))
progress_queue.put((len(sentences), tally, raw_tally)) # report back progress
jobs_processed += 1
logger.debug("worker exiting, processed %i jobs", jobs_processed)
def job_producer():
"""Fill jobs queue using the input `sentences` iterator."""
job_batch, batch_size = [], 0
pushed_words, pushed_examples = 0, 0
next_alpha = self.alpha
job_no = 0
for sent_idx, sentence in enumerate(sentences):
sentence_length = self._raw_word_count([sentence])
# can we fit this sentence into the existing job batch?
if batch_size + sentence_length <= self.batch_words:
# yes => add it to the current job
job_batch.append(sentence)
batch_size += sentence_length
else:
# no => submit the existing job
logger.debug(
"queueing job #%i (%i words, %i sentences) at alpha %.05f",
job_no, batch_size, len(job_batch), next_alpha)
job_no += 1
job_queue.put((job_batch, next_alpha))
# update the learning rate for the next job
if self.min_alpha < next_alpha:
if total_examples:
# examples-based decay
pushed_examples += len(job_batch)
progress = 1.0 * pushed_examples / total_examples
else:
# words-based decay
pushed_words += self._raw_word_count(job_batch)
progress = 1.0 * pushed_words / total_words
next_alpha = self.alpha - (self.alpha - self.min_alpha) * progress
next_alpha = max(self.min_alpha, next_alpha)
# add the sentence that didn't fit as the first item of a new job
job_batch, batch_size = [sentence], sentence_length
# add the last job too (may be significantly smaller than batch_words)
if job_batch:
logger.debug(
"queueing job #%i (%i words, %i sentences) at alpha %.05f",
job_no, batch_size, len(job_batch), next_alpha)
job_no += 1
job_queue.put((job_batch, next_alpha))
if job_no == 0 and self.train_count == 0:
logger.warning(
"train() called with an empty iterator (if not intended, "
"be sure to provide a corpus that offers restartable "
"iteration = an iterable)."
)
# give the workers heads up that they can finish -- no more work!
for _ in xrange(self.workers):
job_queue.put(None)
logger.debug("job loop exiting, total %i jobs", job_no)
# buffer ahead only a limited number of jobs.. this is the reason we can't simply use ThreadPool :(
job_queue = Queue(maxsize=queue_factor * self.workers)
progress_queue = Queue(maxsize=(queue_factor + 1) * self.workers)
workers = [threading.Thread(target=worker_loop) for _ in xrange(self.workers)]
unfinished_worker_count = len(workers)
workers.append(threading.Thread(target=job_producer))
for thread in workers:
thread.daemon = True # make interrupting the process with ctrl+c easier
thread.start()
example_count, trained_word_count, raw_word_count = 0, 0, word_count
start, next_report = default_timer() - 0.00001, 1.0
while unfinished_worker_count > 0:
report = progress_queue.get() # blocks if workers too slow
if report is None: # a thread reporting that it finished
unfinished_worker_count -= 1
logger.info("worker thread finished; awaiting finish of %i more threads", unfinished_worker_count)
continue
examples, trained_words, raw_words = report
job_tally += 1
# update progress stats
example_count += examples
trained_word_count += trained_words # only words in vocab & sampled
raw_word_count += raw_words
# log progress once every report_delay seconds
elapsed = default_timer() - start
if elapsed >= next_report:
if total_examples:
# examples-based progress %
logger.info(
"PROGRESS: at %.2f%% examples, %.0f words/s, in_qsize %i, out_qsize %i",
100.0 * example_count / total_examples, trained_word_count / elapsed,
utils.qsize(job_queue), utils.qsize(progress_queue))
else:
# words-based progress %
logger.info(
"PROGRESS: at %.2f%% words, %.0f words/s, in_qsize %i, out_qsize %i",
100.0 * raw_word_count / total_words, trained_word_count / elapsed,
utils.qsize(job_queue), utils.qsize(progress_queue))
next_report = elapsed + report_delay
# all done; report the final stats
elapsed = default_timer() - start
logger.info(
"training on %i raw words (%i effective words) took %.1fs, %.0f effective words/s",
raw_word_count, trained_word_count, elapsed, trained_word_count / elapsed)
if job_tally < 10 * self.workers:
logger.warn("under 10 jobs per worker: consider setting a smaller `batch_words' for smoother alpha decay")
# check that the input corpus hasn't changed during iteration
if total_examples and total_examples != example_count:
logger.warn("supplied example count (%i) did not equal expected count (%i)", example_count, total_examples)
if total_words and total_words != raw_word_count:
logger.warn("supplied raw word count (%i) did not equal expected count (%i)", raw_word_count, total_words)
self.train_count += 1 # number of times train() has been called
self.total_train_time += elapsed
self.clear_sims()
return trained_word_count
# basics copied from the train() function
def score(self, sentences, total_sentences=int(1e6), chunksize=100, queue_factor=2, report_delay=1):
"""
Score the log probability for a sequence of sentences (can be a once-only generator stream).
Each sentence must be a list of unicode strings.
This does not change the fitted model in any way (see Word2Vec.train() for that)
Note that you should specify total_sentences; we'll run into problems if you ask to
score more than this number of sentences but it is inefficient to set the value too high.
See the article by [taddy]_ and the gensim demo at [deepir]_ for examples of how to use such scores in document classification.
.. [taddy] Taddy, Matt. Document Classification by Inversion of Distributed Language Representations, in Proceedings of the 2015 Conference of the Association of Computational Linguistics.
.. [deepir] https://github.com/TaddyLab/gensim/blob/deepir/docs/notebooks/deepir.ipynb
"""
if FAST_VERSION < 0:
import warnings
warnings.warn("C extension compilation failed, scoring will be slow. "
"Install a C compiler and reinstall gensim for fastness.")
logger.info(
"scoring sentences with %i workers on %i vocabulary and %i features, "
"using sg=%s hs=%s sample=%s and negative=%s",
self.workers, len(self.vocab), self.layer1_size, self.sg, self.hs, self.sample, self.negative)
if not self.vocab:
raise RuntimeError("you must first build vocabulary before scoring new data")
if not self.hs:
raise RuntimeError("we have only implemented score for hs")
def worker_loop():
"""Train the model, lifting lists of sentences from the jobs queue."""
work = zeros(1, dtype=REAL) # for sg hs, we actually only need one memory loc (running sum)
neu1 = matutils.zeros_aligned(self.layer1_size, dtype=REAL)
while True:
job = job_queue.get()
if job is None: # signal to finish
break
ns = 0
for sentence_id, sentence in job:
if sentence_id >= total_sentences:
break
if self.sg:
score = score_sentence_sg(self, sentence, work)
else:
score = score_sentence_cbow(self, sentence, work, neu1)
sentence_scores[sentence_id] = score
ns += 1
progress_queue.put(ns) # report progress
start, next_report = default_timer(), 1.0
# buffer ahead only a limited number of jobs.. this is the reason we can't simply use ThreadPool :(
job_queue = Queue(maxsize=queue_factor * self.workers)
progress_queue = Queue(maxsize=(queue_factor + 1) * self.workers)
workers = [threading.Thread(target=worker_loop) for _ in xrange(self.workers)]
for thread in workers:
thread.daemon = True # make interrupting the process with ctrl+c easier
thread.start()
sentence_count = 0
sentence_scores = matutils.zeros_aligned(total_sentences, dtype=REAL)
push_done = False
done_jobs = 0
jobs_source = enumerate(utils.grouper(enumerate(sentences), chunksize))
# fill jobs queue with (id, sentence) job items
while True:
try:
job_no, items = next(jobs_source)
if (job_no - 1) * chunksize > total_sentences:
logger.warning(
"terminating after %i sentences (set higher total_sentences if you want more).",
total_sentences)
job_no -= 1
raise StopIteration()
logger.debug("putting job #%i in the queue", job_no)
job_queue.put(items)
except StopIteration:
logger.info(
"reached end of input; waiting to finish %i outstanding jobs",
job_no - done_jobs + 1)
for _ in xrange(self.workers):
job_queue.put(None) # give the workers heads up that they can finish -- no more work!
push_done = True
try:
while done_jobs < (job_no + 1) or not push_done:
ns = progress_queue.get(push_done) # only block after all jobs pushed
sentence_count += ns
done_jobs += 1
elapsed = default_timer() - start
if elapsed >= next_report:
logger.info(
"PROGRESS: at %.2f%% sentences, %.0f sentences/s",
100.0 * sentence_count, sentence_count / elapsed)
next_report = elapsed + report_delay # don't flood log, wait report_delay seconds
else:
# loop ended by job count; really done
break
except Empty:
pass # already out of loop; continue to next push
elapsed = default_timer() - start
self.clear_sims()
logger.info(
"scoring %i sentences took %.1fs, %.0f sentences/s",
sentence_count, elapsed, sentence_count / elapsed)
return sentence_scores[:sentence_count]
def clear_sims(self):
self.syn0norm = None
def update_weights(self):
"""
Copy all the existing weights, and reset the weights for the newly
added vocabulary.
"""
logger.info("updating layer weights")
newsyn0 = empty((len(self.vocab), self.vector_size), dtype=REAL)
# copy the weights that are already learned
for i in xrange(0, len(self.syn0)):
newsyn0[i] = deepcopy(self.syn0[i])
# randomize the remaining words
for i in xrange(len(self.vocab), len(newsyn0)):
# construct deterministic seed from word AND seed argument
self.syn0[i] = self.seeded_vector(self.index2word[i] + str(self.seed))
self.syn0 = deepcopy(newsyn0)
if self.hs:
oldsyn1 = deepcopy(self.syn1)
self.syn1 = zeros((len(self.vocab), self.layer1_size), dtype=REAL)
self.syn1[i] = deepcopy(oldsyn1[i])
if self.negative:
oldneg = deepcopy(self.syn1neg)
self.syn1neg = zeros((len(self.vocab), self.layer1_size), dtype=REAL)
self.syn1neg[i] = deepcopy(oldneg[i])
self.syn0norm = None
# do not suppress learning for already learned words
self.syn0_lockf = ones(len(self.vocab), dtype=REAL) # zeros suppress learning
def reset_weights(self):
"""Reset all projection weights to an initial (untrained) state, but keep the existing vocabulary."""
logger.info("resetting layer weights")
self.syn0 = empty((len(self.vocab), self.vector_size), dtype=REAL)
# randomize weights vector by vector, rather than materializing a huge random matrix in RAM at once
for i in xrange(len(self.vocab)):
# construct deterministic seed from word AND seed argument
self.syn0[i] = self.seeded_vector(self.index2word[i] + str(self.seed))
if self.hs:
self.syn1 = zeros((len(self.vocab), self.layer1_size), dtype=REAL)
if self.negative:
self.syn1neg = zeros((len(self.vocab), self.layer1_size), dtype=REAL)
self.syn0norm = None
self.syn0_lockf = ones(len(self.vocab), dtype=REAL) # zeros suppress learning
def seeded_vector(self, seed_string):
"""Create one 'random' vector (but deterministic by seed_string)"""
# Note: built-in hash() may vary by Python version or even (in Py3.x) per launch
once = random.RandomState(self.hashfxn(seed_string) & 0xffffffff)
return (once.rand(self.vector_size) - 0.5) / self.vector_size
def save_word2vec_format(self, fname, fvocab=None, binary=False):
"""
Store the input-hidden weight matrix in the same format used by the original
C word2vec-tool, for compatibility.
"""
if fvocab is not None:
logger.info("storing vocabulary in %s" % (fvocab))
with utils.smart_open(fvocab, 'wb') as vout:
for word, vocab in sorted(iteritems(self.vocab), key=lambda item: -item[1].count):
vout.write(utils.to_utf8("%s %s\n" % (word, vocab.count)))
logger.info("storing %sx%s projection weights into %s" % (len(self.vocab), self.vector_size, fname))
assert (len(self.vocab), self.vector_size) == self.syn0.shape
with utils.smart_open(fname, 'wb') as fout:
fout.write(utils.to_utf8("%s %s\n" % self.syn0.shape))
# store in sorted order: most frequent words at the top
for word, vocab in sorted(iteritems(self.vocab), key=lambda item: -item[1].count):
row = self.syn0[vocab.index]
if binary:
fout.write(utils.to_utf8(word) + b" " + row.tostring())
else:
fout.write(utils.to_utf8("%s %s\n" % (word, ' '.join("%f" % val for val in row))))
@classmethod
def load_word2vec_format(cls, fname, fvocab=None, binary=False, encoding='utf8', unicode_errors='strict'):
"""
Load the input-hidden weight matrix from the original C word2vec-tool format.
Note that the information stored in the file is incomplete (the binary tree is missing),
so while you can query for word similarity etc., you cannot continue training
with a model loaded this way.
`binary` is a boolean indicating whether the data is in binary word2vec format.
`norm_only` is a boolean indicating whether to only store normalised word2vec vectors in memory.
Word counts are read from `fvocab` filename, if set (this is the file generated
by `-save-vocab` flag of the original C tool).
If you trained the C model using non-utf8 encoding for words, specify that
encoding in `encoding`.
"""
counts = None
if fvocab is not None:
logger.info("loading word counts from %s", fvocab)
counts = {}
with utils.smart_open(fvocab) as fin:
for line in fin:
word, count = utils.to_unicode(line).strip().split()
counts[word] = int(count)
logger.info("loading projection weights from %s", fname)
with utils.smart_open(fname) as fin:
header = utils.to_unicode(fin.readline(), encoding=encoding)
vocab_size, vector_size = map(int, header.split()) # throws for invalid file format
result = cls(size=vector_size)
result.syn0 = zeros((vocab_size, vector_size), dtype=REAL)
def add_word(word, weights):
word_id = len(result.vocab)
if word in result.vocab:
logger.warning("duplicate word '%s' in %s, ignoring all but first", word, fname)
return
if counts is None:
# most common scenario: no vocab file given. just make up some bogus counts, in descending order
result.vocab[word] = Vocab(index=word_id, count=vocab_size - word_id)
elif word in counts:
# use count from the vocab file
result.vocab[word] = Vocab(index=word_id, count=counts[word])
else:
# vocab file given, but word is missing -- set count to None (TODO: or raise?)
logger.warning("vocabulary file is incomplete: '%s' is missing", word)
result.vocab[word] = Vocab(index=word_id, count=None)
result.syn0[word_id] = weights
result.index2word.append(word)
if binary:
binary_len = dtype(REAL).itemsize * vector_size
for line_no in xrange(vocab_size):
# mixed text and binary: read text first, then binary
word = []
while True:
ch = fin.read(1)
if ch == b' ':
break
if ch != b'\n': # ignore newlines in front of words (some binary files have)
word.append(ch)
word = utils.to_unicode(b''.join(word), encoding=encoding, errors=unicode_errors)
weights = fromstring(fin.read(binary_len), dtype=REAL)
add_word(word, weights)
else:
for line_no, line in enumerate(fin):
parts = utils.to_unicode(line.rstrip(), encoding=encoding, errors=unicode_errors).split(" ")
if len(parts) != vector_size + 1:
raise ValueError("invalid vector on line %s (is this really the text format?)" % (line_no))
word, weights = parts[0], list(map(REAL, parts[1:]))
add_word(word, weights)
if result.syn0.shape[0] != len(result.vocab):
logger.info(
"duplicate words detected, shrinking matrix size from %i to %i",
result.syn0.shape[0], len(result.vocab)
)
result.syn0 = ascontiguousarray(result.syn0[: len(result.vocab)])
assert (len(result.vocab), result.vector_size) == result.syn0.shape
logger.info("loaded %s matrix from %s" % (result.syn0.shape, fname))
return result
def intersect_word2vec_format(self, fname, binary=False, encoding='utf8', unicode_errors='strict'):
"""
Merge the input-hidden weight matrix from the original C word2vec-tool format
given, where it intersects with the current vocabulary. (No words are added to the
existing vocabulary, but intersecting words adopt the file's weights, and
non-intersecting words are left alone.)
`binary` is a boolean indicating whether the data is in binary word2vec format.
"""
overlap_count = 0
logger.info("loading projection weights from %s" % (fname))
with utils.smart_open(fname) as fin:
header = utils.to_unicode(fin.readline(), encoding=encoding)
vocab_size, vector_size = map(int, header.split()) # throws for invalid file format
if not vector_size == self.vector_size:
raise ValueError("incompatible vector size %d in file %s" % (vector_size, fname))
# TOCONSIDER: maybe mismatched vectors still useful enough to merge (truncating/padding)?
if binary:
binary_len = dtype(REAL).itemsize * vector_size
for line_no in xrange(vocab_size):
# mixed text and binary: read text first, then binary
word = []
while True:
ch = fin.read(1)
if ch == b' ':
break
if ch != b'\n': # ignore newlines in front of words (some binary files have)
word.append(ch)
word = utils.to_unicode(b''.join(word), encoding=encoding, errors=unicode_errors)
weights = fromstring(fin.read(binary_len), dtype=REAL)
if word in self.vocab:
overlap_count += 1
self.syn0[self.vocab[word].index] = weights
self.syn0_lockf[self.vocab[word].index] = 0.0 # lock it
else:
for line_no, line in enumerate(fin):
parts = utils.to_unicode(line.rstrip(), encoding=encoding, errors=unicode_errors).split(" ")
if len(parts) != vector_size + 1:
raise ValueError("invalid vector on line %s (is this really the text format?)" % (line_no))
word, weights = parts[0], list(map(REAL, parts[1:]))
if word in self.vocab:
overlap_count += 1
self.syn0[self.vocab[word].index] = weights
logger.info("merged %d vectors into %s matrix from %s" % (overlap_count, self.syn0.shape, fname))
def most_similar(self, positive=[], negative=[], topn=10, restrict_vocab=None):
"""
Find the top-N most similar words. Positive words contribute positively towards the
similarity, negative words negatively.
This method computes cosine similarity between a simple mean of the projection
weight vectors of the given words and the vectors for each word in the model.
The method corresponds to the `word-analogy` and `distance` scripts in the original
word2vec implementation.
If topn is False, most_similar returns the vector of similarity scores.
`restrict_vocab` is an optional integer which limits the range of vectors which
are searched for most-similar values. For example, restrict_vocab=10000 would
only check the first 10000 word vectors in the vocabulary order. (This may be
meaningful if you've sorted the vocabulary by descending frequency.)
Example::
>>> trained_model.most_similar(positive=['woman', 'king'], negative=['man'])
[('queen', 0.50882536), ...]
"""
self.init_sims()
if isinstance(positive, string_types) and not negative:
# allow calls like most_similar('dog'), as a shorthand for most_similar(['dog'])
positive = [positive]
# add weights for each word, if not already present; default to 1.0 for positive and -1.0 for negative words
positive = [
(word, 1.0) if isinstance(word, string_types + (ndarray,)) else word
for word in positive
]
negative = [
(word, -1.0) if isinstance(word, string_types + (ndarray,)) else word
for word in negative
]
# compute the weighted average of all words
all_words, mean = set(), []
for word, weight in positive + negative:
if isinstance(word, ndarray):
mean.append(weight * word)
elif word in self.vocab:
mean.append(weight * self.syn0norm[self.vocab[word].index])
all_words.add(self.vocab[word].index)
else:
raise KeyError("word '%s' not in vocabulary" % word)
if not mean:
raise ValueError("cannot compute similarity with no input")
mean = matutils.unitvec(array(mean).mean(axis=0)).astype(REAL)
limited = self.syn0norm if restrict_vocab is None else self.syn0norm[:restrict_vocab]
dists = dot(limited, mean)
if not topn:
return dists
best = matutils.argsort(dists, topn=topn + len(all_words), reverse=True)
# ignore (don't return) words from the input
result = [(self.index2word[sim], float(dists[sim])) for sim in best if sim not in all_words]
return result[:topn]
def most_similar_cosmul(self, positive=[], negative=[], topn=10):
"""
Find the top-N most similar words, using the multiplicative combination objective
proposed by Omer Levy and Yoav Goldberg in [4]_. Positive words still contribute
positively towards the similarity, negative words negatively, but with less
susceptibility to one large distance dominating the calculation.
In the common analogy-solving case, of two positive and one negative examples,
this method is equivalent to the "3CosMul" objective (equation (4)) of Levy and Goldberg.
Additional positive or negative examples contribute to the numerator or denominator,
respectively – a potentially sensible but untested extension of the method. (With
a single positive example, rankings will be the same as in the default most_similar.)
Example::
>>> trained_model.most_similar_cosmul(positive=['baghdad', 'england'], negative=['london'])
[(u'iraq', 0.8488819003105164), ...]
.. [4] Omer Levy and Yoav Goldberg. Linguistic Regularities in Sparse and Explicit Word Representations, 2014.
"""
self.init_sims()
if isinstance(positive, string_types) and not negative:
# allow calls like most_similar_cosmul('dog'), as a shorthand for most_similar_cosmul(['dog'])
positive = [positive]
all_words = set()
def word_vec(word):
if isinstance(word, ndarray):
return word
elif word in self.vocab:
all_words.add(self.vocab[word].index)
return self.syn0norm[self.vocab[word].index]
else:
raise KeyError("word '%s' not in vocabulary" % word)
positive = [word_vec(word) for word in positive]
negative = [word_vec(word) for word in negative]
if not positive:
raise ValueError("cannot compute similarity with no input")
# equation (4) of Levy & Goldberg "Linguistic Regularities...",
# with distances shifted to [0,1] per footnote (7)
pos_dists = [((1 + dot(self.syn0norm, term)) / 2) for term in positive]
neg_dists = [((1 + dot(self.syn0norm, term)) / 2) for term in negative]
dists = prod(pos_dists, axis=0) / (prod(neg_dists, axis=0) + 0.000001)
if not topn:
return dists
best = matutils.argsort(dists, topn=topn + len(all_words), reverse=True)
# ignore (don't return) words from the input
result = [(self.index2word[sim], float(dists[sim])) for sim in best if sim not in all_words]
return result[:topn]
def doesnt_match(self, words):
"""
Which word from the given list doesn't go with the others?
Example::
>>> trained_model.doesnt_match("breakfast cereal dinner lunch".split())
'cereal'
"""
self.init_sims()
words = [word for word in words if word in self.vocab] # filter out OOV words
logger.debug("using words %s" % words)
if not words:
raise ValueError("cannot select a word from an empty list")
vectors = vstack(self.syn0norm[self.vocab[word].index] for word in words).astype(REAL)
mean = matutils.unitvec(vectors.mean(axis=0)).astype(REAL)
dists = dot(vectors, mean)
return sorted(zip(dists, words))[0][1]
def __getitem__(self, words):
"""
Accept a single word or a list of words as input.
If a single word: returns the word's representations in vector space, as
a 1D numpy array.
Multiple words: return the words' representations in vector space, as a
2d numpy array: #words x #vector_size. Matrix rows are in the same order
as in input.
Example::
>>> trained_model['office']
array([ -1.40128313e-02, ...])
>>> trained_model[['office', 'products']]
array([ -1.40128313e-02, ...]
[ -1.70425311e-03, ...]
...)
"""
if isinstance(words, string_types):
# allow calls like trained_model['office'], as a shorthand for trained_model[['office']]
return self.syn0[self.vocab[words].index]
return vstack([self.syn0[self.vocab[word].index] for word in words])
def __contains__(self, word):
return word in self.vocab
def similarity(self, w1, w2):
"""
Compute cosine similarity between two words.
Example::
>>> trained_model.similarity('woman', 'man')
0.73723527
>>> trained_model.similarity('woman', 'woman')
1.0
"""
return dot(matutils.unitvec(self[w1]), matutils.unitvec(self[w2]))
def n_similarity(self, ws1, ws2):
"""
Compute cosine similarity between two sets of words.
Example::
>>> trained_model.n_similarity(['sushi', 'shop'], ['japanese', 'restaurant'])
0.61540466561049689
>>> trained_model.n_similarity(['restaurant', 'japanese'], ['japanese', 'restaurant'])
1.0000000000000004
>>> trained_model.n_similarity(['sushi'], ['restaurant']) == trained_model.similarity('sushi', 'restaurant')
True
"""
v1 = [self[word] for word in ws1]
v2 = [self[word] for word in ws2]
return dot(matutils.unitvec(array(v1).mean(axis=0)), matutils.unitvec(array(v2).mean(axis=0)))
def init_sims(self, replace=False):
"""
Precompute L2-normalized vectors.
If `replace` is set, forget the original vectors and only keep the normalized
ones = saves lots of memory!
Note that you **cannot continue training** after doing a replace. The model becomes
effectively read-only = you can call `most_similar`, `similarity` etc., but not `train`.
"""
if getattr(self, 'syn0norm', None) is None or replace:
logger.info("precomputing L2-norms of word weight vectors")
if replace:
for i in xrange(self.syn0.shape[0]):
self.syn0[i, :] /= sqrt((self.syn0[i, :] ** 2).sum(-1))
self.syn0norm = self.syn0
if hasattr(self, 'syn1'):
del self.syn1
else:
self.syn0norm = (self.syn0 / sqrt((self.syn0 ** 2).sum(-1))[..., newaxis]).astype(REAL)
def estimate_memory(self, vocab_size=None, report=None):
"""Estimate required memory for a model using current settings and provided vocabulary size."""
vocab_size = vocab_size or len(self.vocab)
report = report or {}
report['vocab'] = vocab_size * (700 if self.hs else 500)
report['syn0'] = vocab_size * self.vector_size * dtype(REAL).itemsize
if self.hs:
report['syn1'] = vocab_size * self.layer1_size * dtype(REAL).itemsize
if self.negative:
report['syn1neg'] = vocab_size * self.layer1_size * dtype(REAL).itemsize
report['total'] = sum(report.values())
logger.info("estimated required memory for %i words and %i dimensions: %i bytes",
vocab_size, self.vector_size, report['total'])
return report
@staticmethod
def log_accuracy(section):
correct, incorrect = len(section['correct']), len(section['incorrect'])
if correct + incorrect > 0:
logger.info("%s: %.1f%% (%i/%i)" %
(section['section'], 100.0 * correct / (correct + incorrect),
correct, correct + incorrect))
def accuracy(self, questions, restrict_vocab=30000, most_similar=most_similar):
"""
Compute accuracy of the model. `questions` is a filename where lines are
4-tuples of words, split into sections by ": SECTION NAME" lines.
See https://code.google.com/p/word2vec/source/browse/trunk/questions-words.txt for an example.
The accuracy is reported (=printed to log and returned as a list) for each
section separately, plus there's one aggregate summary at the end.
Use `restrict_vocab` to ignore all questions containing a word whose frequency
is not in the top-N most frequent words (default top 30,000).
This method corresponds to the `compute-accuracy` script of the original C word2vec.
"""
ok_vocab = dict(sorted(iteritems(self.vocab),
key=lambda item: -item[1].count)[:restrict_vocab])
ok_index = set(v.index for v in itervalues(ok_vocab))
sections, section = [], None
for line_no, line in enumerate(utils.smart_open(questions)):
# TODO: use level3 BLAS (=evaluate multiple questions at once), for speed
line = utils.to_unicode(line)
if line.startswith(': '):
# a new section starts => store the old section
if section:
sections.append(section)
self.log_accuracy(section)
section = {'section': line.lstrip(': ').strip(), 'correct': [], 'incorrect': []}
else:
if not section:
raise ValueError("missing section header before line #%i in %s" % (line_no, questions))
try:
a, b, c, expected = [word.lower() for word in line.split()] # TODO assumes vocabulary preprocessing uses lowercase, too...
except:
logger.info("skipping invalid line #%i in %s" % (line_no, questions))
if a not in ok_vocab or b not in ok_vocab or c not in ok_vocab or expected not in ok_vocab:
logger.debug("skipping line #%i with OOV words: %s" % (line_no, line.strip()))
continue
ignore = set(self.vocab[v].index for v in [a, b, c]) # indexes of words to ignore
predicted = None
# find the most likely prediction, ignoring OOV words and input words
sims = most_similar(self, positive=[b, c], negative=[a], topn=False, restrict_vocab=restrict_vocab)
for index in matutils.argsort(sims, reverse=True):
if index in ok_index and index not in ignore:
predicted = self.index2word[index]
if predicted != expected:
logger.debug("%s: expected %s, predicted %s", line.strip(), expected, predicted)
break
if predicted == expected:
section['correct'].append((a, b, c, expected))
else:
section['incorrect'].append((a, b, c, expected))
if section:
# store the last section, too
sections.append(section)
self.log_accuracy(section)
total = {
'section': 'total',
'correct': sum((s['correct'] for s in sections), []),
'incorrect': sum((s['incorrect'] for s in sections), []),
}
self.log_accuracy(total)
sections.append(total)
return sections
def __str__(self):
return "%s(vocab=%s, size=%s, alpha=%s)" % (self.__class__.__name__, len(self.index2word), self.vector_size, self.alpha)
def save(self, *args, **kwargs):
# don't bother storing the cached normalized vectors, recalculable table
kwargs['ignore'] = kwargs.get('ignore', ['syn0norm', 'table', 'cum_table'])
super(Word2Vec, self).save(*args, **kwargs)
save.__doc__ = utils.SaveLoad.save.__doc__
@classmethod
def load(cls, *args, **kwargs):
model = super(Word2Vec, cls).load(*args, **kwargs)
# update older models
if hasattr(model, 'table'):
delattr(model, 'table') # discard in favor of cum_table
if model.negative and hasattr(model, 'index2word'):
model.make_cum_table() # rebuild cum_table from vocabulary
if not hasattr(model, 'corpus_count'):
model.corpus_count = None
for v in model.vocab.values():
if hasattr(v, 'sample_int'):
break # already 0.12.0+ style int probabilities
elif hasattr(v, 'sample_probability'):
v.sample_int = int(round(v.sample_probability * 2**32))
del v.sample_probability
if not hasattr(model, 'syn0_lockf') and hasattr(model, 'syn0'):
model.syn0_lockf = ones(len(model.syn0), dtype=REAL)
if not hasattr(model, 'random'):
model.random = random.RandomState(model.seed)
if not hasattr(model, 'train_count'):
model.train_count = 0
model.total_train_time = 0
return model
class BrownCorpus(object):
"""Iterate over sentences from the Brown corpus (part of NLTK data)."""
def __init__(self, dirname):
self.dirname = dirname
def __iter__(self):
for fname in os.listdir(self.dirname):
fname = os.path.join(self.dirname, fname)
if not os.path.isfile(fname):
continue
for line in utils.smart_open(fname):
line = utils.to_unicode(line)
# each file line is a single sentence in the Brown corpus
# each token is WORD/POS_TAG
token_tags = [t.split('/') for t in line.split() if len(t.split('/')) == 2]
# ignore words with non-alphabetic tags like ",", "!" etc (punctuation, weird stuff)
words = ["%s/%s" % (token.lower(), tag[:2]) for token, tag in token_tags if tag[:2].isalpha()]
if not words: # don't bother sending out empty sentences
continue
yield words
class Text8Corpus(object):
"""Iterate over sentences from the "text8" corpus, unzipped from http://mattmahoney.net/dc/text8.zip ."""
def __init__(self, fname, max_sentence_length=MAX_WORDS_IN_BATCH):
self.fname = fname
self.max_sentence_length = max_sentence_length
def __iter__(self):
# the entire corpus is one gigantic line -- there are no sentence marks at all
# so just split the sequence of tokens arbitrarily: 1 sentence = 1000 tokens
sentence, rest = [], b''
with utils.smart_open(self.fname) as fin:
while True:
text = rest + fin.read(8192) # avoid loading the entire file (=1 line) into RAM
if text == rest: # EOF
sentence.extend(rest.split()) # return the last chunk of words, too (may be shorter/longer)
if sentence:
yield sentence
break
last_token = text.rfind(b' ') # last token may have been split in two... keep for next iteration
words, rest = (utils.to_unicode(text[:last_token]).split(),
text[last_token:].strip()) if last_token >= 0 else ([], text)
sentence.extend(words)
while len(sentence) >= self.max_sentence_length:
yield sentence[:self.max_sentence_length]
sentence = sentence[self.max_sentence_length:]
class LineSentence(object):
"""
Simple format: one sentence = one line; words already preprocessed and separated by whitespace.
"""
def __init__(self, source, max_sentence_length=MAX_WORDS_IN_BATCH, limit=None):
"""
`source` can be either a string or a file object. Clip the file to the first
`limit` lines (or no clipped if limit is None, the default).
Example::
sentences = LineSentence('myfile.txt')
Or for compressed files::
sentences = LineSentence('compressed_text.txt.bz2')
sentences = LineSentence('compressed_text.txt.gz')
"""
self.source = source
self.max_sentence_length = max_sentence_length
self.limit = limit
def __iter__(self):
"""Iterate through the lines in the source."""
try:
# Assume it is a file-like object and try treating it as such
# Things that don't have seek will trigger an exception
self.source.seek(0)
for line in itertools.islice(self.source, self.limit):
line = utils.to_unicode(line).split()
i = 0
while i < len(line):
yield line[i : i + self.max_sentence_length]
i += self.max_sentence_length
except AttributeError:
# If it didn't work like a file, use it as a string filename
with utils.smart_open(self.source) as fin:
for line in itertools.islice(fin, self.limit):
line = utils.to_unicode(line).split()
i = 0
while i < len(line):
yield line[i : i + self.max_sentence_length]
i += self.max_sentence_length
# Example: ./word2vec.py -train data.txt -output vec.txt -size 200 -window 5 -sample 1e-4 -negative 5 -hs 0 -binary 0 -cbow 1 -iter 3
if __name__ == "__main__":
import argparse
logging.basicConfig(
format='%(asctime)s : %(threadName)s : %(levelname)s : %(message)s',
level=logging.INFO)
logging.info("running %s", " ".join(sys.argv))
logging.info("using optimization %s", FAST_VERSION)
# check and process cmdline input
program = os.path.basename(sys.argv[0])
if len(sys.argv) < 2:
print(globals()['__doc__'] % locals())
sys.exit(1)
from gensim.models.word2vec import Word2Vec # avoid referencing __main__ in pickle
seterr(all='raise') # don't ignore numpy errors
parser = argparse.ArgumentParser()
parser.add_argument("-train", help="Use text data from file TRAIN to train the model", required=True)
parser.add_argument("-output", help="Use file OUTPUT to save the resulting word vectors")
parser.add_argument("-window", help="Set max skip length WINDOW between words; default is 5", type=int, default=5)
parser.add_argument("-size", help="Set size of word vectors; default is 100", type=int, default=100)
parser.add_argument("-sample", help="Set threshold for occurrence of words. Those that appear with higher frequency in the training data will be randomly down-sampled; default is 1e-3, useful range is (0, 1e-5)", type=float, default=1e-3)
parser.add_argument("-hs", help="Use Hierarchical Softmax; default is 0 (not used)", type=int, default=0, choices=[0, 1])
parser.add_argument("-negative", help="Number of negative examples; default is 5, common values are 3 - 10 (0 = not used)", type=int, default=5)
parser.add_argument("-threads", help="Use THREADS threads (default 12)", type=int, default=12)
parser.add_argument("-iter", help="Run more training iterations (default 5)", type=int, default=5)
parser.add_argument("-min_count", help="This will discard words that appear less than MIN_COUNT times; default is 5", type=int, default=5)
parser.add_argument("-cbow", help="Use the continuous bag of words model; default is 1 (use 0 for skip-gram model)", type=int, default=1, choices=[0, 1])
parser.add_argument("-binary", help="Save the resulting vectors in binary mode; default is 0 (off)", type=int, default=0, choices=[0, 1])
parser.add_argument("-accuracy", help="Use questions from file ACCURACY to evaluate the model")
args = parser.parse_args()
if args.cbow == 0:
skipgram = 1
else:
skipgram = 0
corpus = LineSentence(args.train)
model = Word2Vec(corpus, size=args.size, min_count=args.min_count, workers=args.threads, window=args.window,sample=args.sample,sg=skipgram,hs=args.hs,negative=args.negative,cbow_mean=1,iter=args.iter)
if args.output:
outfile = args.output
model.save_word2vec_format(outfile, binary=args.binary)
else:
outfile = args.train
model.save(outfile + '.model')
if args.binary == 1:
model.save_word2vec_format(outfile + '.model.bin', binary=True)
else:
model.save_word2vec_format(outfile + '.model.txt', binary=False)
if args.accuracy:
questions_file = args.accuracy
model.accuracy(questions_file)
logger.info("finished running %s", program)
|
zclfly/gensim
|
gensim/models/word2vec.py
|
Python
|
gpl-3.0
| 81,199
|
[
"VisIt"
] |
8b7c19148254812b6cd9d15650722eebf28681c3e20965fd5963b5bda924a759
|
# mako/parsetree.py
# Copyright 2006-2021 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""defines the parse tree components for Mako templates."""
import re
from mako import ast
from mako import exceptions
from mako import filters
from mako import util
class Node:
"""base class for a Node in the parse tree."""
def __init__(self, source, lineno, pos, filename):
self.source = source
self.lineno = lineno
self.pos = pos
self.filename = filename
@property
def exception_kwargs(self):
return {
"source": self.source,
"lineno": self.lineno,
"pos": self.pos,
"filename": self.filename,
}
def get_children(self):
return []
def accept_visitor(self, visitor):
def traverse(node):
for n in node.get_children():
n.accept_visitor(visitor)
method = getattr(visitor, "visit" + self.__class__.__name__, traverse)
method(self)
class TemplateNode(Node):
"""a 'container' node that stores the overall collection of nodes."""
def __init__(self, filename):
super().__init__("", 0, 0, filename)
self.nodes = []
self.page_attributes = {}
def get_children(self):
return self.nodes
def __repr__(self):
return "TemplateNode(%s, %r)" % (
util.sorted_dict_repr(self.page_attributes),
self.nodes,
)
class ControlLine(Node):
"""defines a control line, a line-oriented python line or end tag.
e.g.::
% if foo:
(markup)
% endif
"""
has_loop_context = False
def __init__(self, keyword, isend, text, **kwargs):
super().__init__(**kwargs)
self.text = text
self.keyword = keyword
self.isend = isend
self.is_primary = keyword in ["for", "if", "while", "try", "with"]
self.nodes = []
if self.isend:
self._declared_identifiers = []
self._undeclared_identifiers = []
else:
code = ast.PythonFragment(text, **self.exception_kwargs)
self._declared_identifiers = code.declared_identifiers
self._undeclared_identifiers = code.undeclared_identifiers
def get_children(self):
return self.nodes
def declared_identifiers(self):
return self._declared_identifiers
def undeclared_identifiers(self):
return self._undeclared_identifiers
def is_ternary(self, keyword):
"""return true if the given keyword is a ternary keyword
for this ControlLine"""
cases = {
"if": {"else", "elif"},
"try": {"except", "finally"},
"for": {"else"},
}
return keyword in cases.get(self.keyword, set())
def __repr__(self):
return "ControlLine(%r, %r, %r, %r)" % (
self.keyword,
self.text,
self.isend,
(self.lineno, self.pos),
)
class Text(Node):
"""defines plain text in the template."""
def __init__(self, content, **kwargs):
super().__init__(**kwargs)
self.content = content
def __repr__(self):
return "Text(%r, %r)" % (self.content, (self.lineno, self.pos))
class Code(Node):
"""defines a Python code block, either inline or module level.
e.g.::
inline:
<%
x = 12
%>
module level:
<%!
import logger
%>
"""
def __init__(self, text, ismodule, **kwargs):
super().__init__(**kwargs)
self.text = text
self.ismodule = ismodule
self.code = ast.PythonCode(text, **self.exception_kwargs)
def declared_identifiers(self):
return self.code.declared_identifiers
def undeclared_identifiers(self):
return self.code.undeclared_identifiers
def __repr__(self):
return "Code(%r, %r, %r)" % (
self.text,
self.ismodule,
(self.lineno, self.pos),
)
class Comment(Node):
"""defines a comment line.
# this is a comment
"""
def __init__(self, text, **kwargs):
super().__init__(**kwargs)
self.text = text
def __repr__(self):
return "Comment(%r, %r)" % (self.text, (self.lineno, self.pos))
class Expression(Node):
"""defines an inline expression.
${x+y}
"""
def __init__(self, text, escapes, **kwargs):
super().__init__(**kwargs)
self.text = text
self.escapes = escapes
self.escapes_code = ast.ArgumentList(escapes, **self.exception_kwargs)
self.code = ast.PythonCode(text, **self.exception_kwargs)
def declared_identifiers(self):
return []
def undeclared_identifiers(self):
# TODO: make the "filter" shortcut list configurable at parse/gen time
return self.code.undeclared_identifiers.union(
self.escapes_code.undeclared_identifiers.difference(
filters.DEFAULT_ESCAPES
)
).difference(self.code.declared_identifiers)
def __repr__(self):
return "Expression(%r, %r, %r)" % (
self.text,
self.escapes_code.args,
(self.lineno, self.pos),
)
class _TagMeta(type):
"""metaclass to allow Tag to produce a subclass according to
its keyword"""
_classmap = {}
def __init__(cls, clsname, bases, dict_):
if getattr(cls, "__keyword__", None) is not None:
cls._classmap[cls.__keyword__] = cls
super().__init__(clsname, bases, dict_)
def __call__(cls, keyword, attributes, **kwargs):
if ":" in keyword:
ns, defname = keyword.split(":")
return type.__call__(
CallNamespaceTag, ns, defname, attributes, **kwargs
)
try:
cls = _TagMeta._classmap[keyword]
except KeyError:
raise exceptions.CompileException(
"No such tag: '%s'" % keyword,
source=kwargs["source"],
lineno=kwargs["lineno"],
pos=kwargs["pos"],
filename=kwargs["filename"],
)
return type.__call__(cls, keyword, attributes, **kwargs)
class Tag(Node, metaclass=_TagMeta):
"""abstract base class for tags.
e.g.::
<%sometag/>
<%someothertag>
stuff
</%someothertag>
"""
__keyword__ = None
def __init__(
self,
keyword,
attributes,
expressions,
nonexpressions,
required,
**kwargs,
):
r"""construct a new Tag instance.
this constructor not called directly, and is only called
by subclasses.
:param keyword: the tag keyword
:param attributes: raw dictionary of attribute key/value pairs
:param expressions: a set of identifiers that are legal attributes,
which can also contain embedded expressions
:param nonexpressions: a set of identifiers that are legal
attributes, which cannot contain embedded expressions
:param \**kwargs:
other arguments passed to the Node superclass (lineno, pos)
"""
super().__init__(**kwargs)
self.keyword = keyword
self.attributes = attributes
self._parse_attributes(expressions, nonexpressions)
missing = [r for r in required if r not in self.parsed_attributes]
if len(missing):
raise exceptions.CompileException(
(
"Missing attribute(s): %s"
% ",".join(repr(m) for m in missing)
),
**self.exception_kwargs,
)
self.parent = None
self.nodes = []
def is_root(self):
return self.parent is None
def get_children(self):
return self.nodes
def _parse_attributes(self, expressions, nonexpressions):
undeclared_identifiers = set()
self.parsed_attributes = {}
for key in self.attributes:
if key in expressions:
expr = []
for x in re.compile(r"(\${.+?})", re.S).split(
self.attributes[key]
):
m = re.compile(r"^\${(.+?)}$", re.S).match(x)
if m:
code = ast.PythonCode(
m.group(1).rstrip(), **self.exception_kwargs
)
# we aren't discarding "declared_identifiers" here,
# which we do so that list comprehension-declared
# variables aren't counted. As yet can't find a
# condition that requires it here.
undeclared_identifiers = undeclared_identifiers.union(
code.undeclared_identifiers
)
expr.append("(%s)" % m.group(1))
elif x:
expr.append(repr(x))
self.parsed_attributes[key] = " + ".join(expr) or repr("")
elif key in nonexpressions:
if re.search(r"\${.+?}", self.attributes[key]):
raise exceptions.CompileException(
"Attribute '%s' in tag '%s' does not allow embedded "
"expressions" % (key, self.keyword),
**self.exception_kwargs,
)
self.parsed_attributes[key] = repr(self.attributes[key])
else:
raise exceptions.CompileException(
"Invalid attribute for tag '%s': '%s'"
% (self.keyword, key),
**self.exception_kwargs,
)
self.expression_undeclared_identifiers = undeclared_identifiers
def declared_identifiers(self):
return []
def undeclared_identifiers(self):
return self.expression_undeclared_identifiers
def __repr__(self):
return "%s(%r, %s, %r, %r)" % (
self.__class__.__name__,
self.keyword,
util.sorted_dict_repr(self.attributes),
(self.lineno, self.pos),
self.nodes,
)
class IncludeTag(Tag):
__keyword__ = "include"
def __init__(self, keyword, attributes, **kwargs):
super().__init__(
keyword,
attributes,
("file", "import", "args"),
(),
("file",),
**kwargs,
)
self.page_args = ast.PythonCode(
"__DUMMY(%s)" % attributes.get("args", ""), **self.exception_kwargs
)
def declared_identifiers(self):
return []
def undeclared_identifiers(self):
identifiers = self.page_args.undeclared_identifiers.difference(
{"__DUMMY"}
).difference(self.page_args.declared_identifiers)
return identifiers.union(super().undeclared_identifiers())
class NamespaceTag(Tag):
__keyword__ = "namespace"
def __init__(self, keyword, attributes, **kwargs):
super().__init__(
keyword,
attributes,
("file",),
("name", "inheritable", "import", "module"),
(),
**kwargs,
)
self.name = attributes.get("name", "__anon_%s" % hex(abs(id(self))))
if "name" not in attributes and "import" not in attributes:
raise exceptions.CompileException(
"'name' and/or 'import' attributes are required "
"for <%namespace>",
**self.exception_kwargs,
)
if "file" in attributes and "module" in attributes:
raise exceptions.CompileException(
"<%namespace> may only have one of 'file' or 'module'",
**self.exception_kwargs,
)
def declared_identifiers(self):
return []
class TextTag(Tag):
__keyword__ = "text"
def __init__(self, keyword, attributes, **kwargs):
super().__init__(keyword, attributes, (), ("filter"), (), **kwargs)
self.filter_args = ast.ArgumentList(
attributes.get("filter", ""), **self.exception_kwargs
)
def undeclared_identifiers(self):
return self.filter_args.undeclared_identifiers.difference(
filters.DEFAULT_ESCAPES.keys()
).union(self.expression_undeclared_identifiers)
class DefTag(Tag):
__keyword__ = "def"
def __init__(self, keyword, attributes, **kwargs):
expressions = ["buffered", "cached"] + [
c for c in attributes if c.startswith("cache_")
]
super().__init__(
keyword,
attributes,
expressions,
("name", "filter", "decorator"),
("name",),
**kwargs,
)
name = attributes["name"]
if re.match(r"^[\w_]+$", name):
raise exceptions.CompileException(
"Missing parenthesis in %def", **self.exception_kwargs
)
self.function_decl = ast.FunctionDecl(
"def " + name + ":pass", **self.exception_kwargs
)
self.name = self.function_decl.funcname
self.decorator = attributes.get("decorator", "")
self.filter_args = ast.ArgumentList(
attributes.get("filter", ""), **self.exception_kwargs
)
is_anonymous = False
is_block = False
@property
def funcname(self):
return self.function_decl.funcname
def get_argument_expressions(self, **kw):
return self.function_decl.get_argument_expressions(**kw)
def declared_identifiers(self):
return self.function_decl.allargnames
def undeclared_identifiers(self):
res = []
for c in self.function_decl.defaults:
res += list(
ast.PythonCode(
c, **self.exception_kwargs
).undeclared_identifiers
)
return (
set(res)
.union(
self.filter_args.undeclared_identifiers.difference(
filters.DEFAULT_ESCAPES.keys()
)
)
.union(self.expression_undeclared_identifiers)
.difference(self.function_decl.allargnames)
)
class BlockTag(Tag):
__keyword__ = "block"
def __init__(self, keyword, attributes, **kwargs):
expressions = ["buffered", "cached", "args"] + [
c for c in attributes if c.startswith("cache_")
]
super().__init__(
keyword,
attributes,
expressions,
("name", "filter", "decorator"),
(),
**kwargs,
)
name = attributes.get("name")
if name and not re.match(r"^[\w_]+$", name):
raise exceptions.CompileException(
"%block may not specify an argument signature",
**self.exception_kwargs,
)
if not name and attributes.get("args", None):
raise exceptions.CompileException(
"Only named %blocks may specify args", **self.exception_kwargs
)
self.body_decl = ast.FunctionArgs(
attributes.get("args", ""), **self.exception_kwargs
)
self.name = name
self.decorator = attributes.get("decorator", "")
self.filter_args = ast.ArgumentList(
attributes.get("filter", ""), **self.exception_kwargs
)
is_block = True
@property
def is_anonymous(self):
return self.name is None
@property
def funcname(self):
return self.name or "__M_anon_%d" % (self.lineno,)
def get_argument_expressions(self, **kw):
return self.body_decl.get_argument_expressions(**kw)
def declared_identifiers(self):
return self.body_decl.allargnames
def undeclared_identifiers(self):
return (
self.filter_args.undeclared_identifiers.difference(
filters.DEFAULT_ESCAPES.keys()
)
).union(self.expression_undeclared_identifiers)
class CallTag(Tag):
__keyword__ = "call"
def __init__(self, keyword, attributes, **kwargs):
super().__init__(
keyword, attributes, ("args"), ("expr",), ("expr",), **kwargs
)
self.expression = attributes["expr"]
self.code = ast.PythonCode(self.expression, **self.exception_kwargs)
self.body_decl = ast.FunctionArgs(
attributes.get("args", ""), **self.exception_kwargs
)
def declared_identifiers(self):
return self.code.declared_identifiers.union(self.body_decl.allargnames)
def undeclared_identifiers(self):
return self.code.undeclared_identifiers.difference(
self.code.declared_identifiers
)
class CallNamespaceTag(Tag):
def __init__(self, namespace, defname, attributes, **kwargs):
super().__init__(
namespace + ":" + defname,
attributes,
tuple(attributes.keys()) + ("args",),
(),
(),
**kwargs,
)
self.expression = "%s.%s(%s)" % (
namespace,
defname,
",".join(
"%s=%s" % (k, v)
for k, v in self.parsed_attributes.items()
if k != "args"
),
)
self.code = ast.PythonCode(self.expression, **self.exception_kwargs)
self.body_decl = ast.FunctionArgs(
attributes.get("args", ""), **self.exception_kwargs
)
def declared_identifiers(self):
return self.code.declared_identifiers.union(self.body_decl.allargnames)
def undeclared_identifiers(self):
return self.code.undeclared_identifiers.difference(
self.code.declared_identifiers
)
class InheritTag(Tag):
__keyword__ = "inherit"
def __init__(self, keyword, attributes, **kwargs):
super().__init__(
keyword, attributes, ("file",), (), ("file",), **kwargs
)
class PageTag(Tag):
__keyword__ = "page"
def __init__(self, keyword, attributes, **kwargs):
expressions = [
"cached",
"args",
"expression_filter",
"enable_loop",
] + [c for c in attributes if c.startswith("cache_")]
super().__init__(keyword, attributes, expressions, (), (), **kwargs)
self.body_decl = ast.FunctionArgs(
attributes.get("args", ""), **self.exception_kwargs
)
self.filter_args = ast.ArgumentList(
attributes.get("expression_filter", ""), **self.exception_kwargs
)
def declared_identifiers(self):
return self.body_decl.allargnames
|
sqlalchemy/mako
|
mako/parsetree.py
|
Python
|
mit
| 19,007
|
[
"VisIt"
] |
e1243dadd7cdbd74bedea66f6f5703f0a5925f21091a110a73d4af35fcb8a286
|
# coding: utf-8
'''
-----------------------------------------------------------------------------
Copyright 2015 Esri
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-----------------------------------------------------------------------------
==================================================
DeleteOldFiles.py
--------------------------------------------------
requirements: ArcGIS 10.3+, Python 2.7
author: ArcGIS Solutions
company: Esri
==================================================
description:
Deletes old NETCDF files from a directory specified by the user
for a time period specified by a user
==================================================
history:
3/24/2015 - AB - Original development
12/3/2015 - MF - Updates for standards
==================================================
'''
import os
import time
import arcpy
# Input path from which files should be deleted.
path = arcpy.GetParameterAsText(0)
# number of days to remove
days = arcpy.GetParameter(1)
# Get the present time
now = time.time()
# Get the list of files within the directory.
for f in os.listdir(path):
f = os.path.join(path, f)
#get the last modified time for each of the files and compare this to the date 7 days ago.
if os.stat(f).st_mtime < now - days * 86400:
if os.path.isfile(f):
#If the file is older than specified age then delete it.
#TODO: Check that we are removing a NetCDF (*.nc) file, and not something else?
os.remove(f)
print(f)
arcpy.AddMessage(f)
print("Specified files deleted")
arcpy.AddMessage("Specified files deleted")
|
jfrygeo/solutions-geoprocessing-toolbox
|
suitability/toolboxes/scripts/DeleteOldFiles.py
|
Python
|
apache-2.0
| 2,088
|
[
"NetCDF"
] |
e6b60e90d772582635e22cfdc61571650ced7afa77927e23bec852d51f03ab68
|
from ase import Atom
from ase.units import Hartree
from gpaw import GPAW, FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h =.3
box = 4.
energy_tolerance = 0.0004
l=2 # d-orbitals
U_ev=3 # U in eV
U_au=U_ev / Hartree # U in atomic units
scale=1 # Do not scale (does not seem to matter much)
store=0 # Do not store (not in use yet)
s = Cluster([Atom('Zn')])
s.minimal_box(box, h=h)
E = {}
E_U = {}
for spin in [0, 1]:
c = GPAW(h=h, spinpol=bool(spin),
charge=1, occupations=FermiDirac(width=0.1)
)
s.set_calculator(c)
E[spin] = s.get_potential_energy()
for setup in c.hamiltonian.setups:
setup.set_hubbard_u(U_au, l, scale, store) # Apply U
c.scf.reset()
E_U[spin] = s.get_potential_energy()
print "E=", E
equal(E[0], E[1], energy_tolerance)
print "E_U=", E_U
equal(E_U[0], E_U[1], energy_tolerance)
|
qsnake/gpaw
|
gpaw/test/Hubbard_U_Zn.py
|
Python
|
gpl-3.0
| 975
|
[
"ASE",
"GPAW"
] |
fd9fa1bebf72599b9b29f4448a2758252d81358e189ec780bcd18f9ed15ed212
|
"""A medical image analysis pipeline.
The pipeline is used for brain tissue segmentation using a decision forest classifier.
"""
import argparse
import datetime
import os
import sys
import timeit
import SimpleITK as sitk
import numpy as np
from tensorflow.python.platform import app
from sklearn.mixture import GaussianMixture
from scipy import stats as scipy_stats
sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), '..')) # append the MIALab root directory to Python path
# fixes the ModuleNotFoundError when executing main.py in the console after code changes (e.g. git pull)
# somehow pip install does not keep track of packages
import mialab.classifier.decision_forest as df
import mialab.data.conversion as conversion
import mialab.data.structure as structure
import mialab.data.loading as load
import mialab.utilities.file_access_utilities as futil
import mialab.utilities.pipeline_utilities as putil
import mialab.utilities.statistic_utilities as statistics
FLAGS = None # the program flags
IMAGE_KEYS = [structure.BrainImageTypes.T1, structure.BrainImageTypes.T2, structure.BrainImageTypes.GroundTruth] # the list of images we will load
TEST_BATCH_SIZE = 2 # 1..30, the higher the faster but more memory usage
NORMALIZE_FEATURES = False # Normalize feature vectors to mean 0 and std 1
def main(_):
"""Brain tissue segmentation using decision forests.
The main routine executes the medical image analysis pipeline:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(FLAGS.data_atlas_dir)
print('-' * 5, 'Training...')
# generate a model directory (use datetime to ensure that the directory is empty)
# we need an empty directory because TensorFlow will continue training an existing model if it is not empty
t = datetime.datetime.now().strftime('%Y-%m-%d%H%M%S')
model_dir = os.path.join(FLAGS.model_dir, t)
os.makedirs(model_dir, exist_ok=True)
# crawl the training image directories
crawler = load.FileSystemDataCrawler(FLAGS.data_train_dir,
IMAGE_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
data_items = list(crawler.data.items())
train_data_size = len(data_items)
pre_process_params = {'zscore_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True}
start_time_total_train = timeit.default_timer()
batch_data = dict(data_items)
# load images for training and pre-process
images = putil.pre_process_batch(batch_data, pre_process_params, multi_process=True)
print('pre-processing done')
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1] for img in images])
if NORMALIZE_FEATURES:
# normalize data (mean 0, std 1)
data_train = scipy_stats.zscore(data_train)
start_time = timeit.default_timer()
# Gaussian mixture model
# ##############################################################################################################
thegmm = GaussianMixture(n_components=3, covariance_type='tied')
thegmm.fit(data_train, labels_train)
# ##############################################################################################################
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
time_total_train = timeit.default_timer() - start_time_total_train
start_time_total_test = timeit.default_timer()
print('-' * 5, 'Testing...')
result_dir = os.path.join(FLAGS.result_dir, t)
os.makedirs(result_dir, exist_ok=True)
# initialize evaluator
evaluator = putil.init_evaluator(result_dir)
# crawl the training image directories
crawler = load.FileSystemDataCrawler(FLAGS.data_test_dir,
IMAGE_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
data_items = list(crawler.data.items())
all_probabilities = None
for batch_index in range(0, len(data_items), TEST_BATCH_SIZE):
# slicing manages out of range; no need to worry
batch_data = dict(data_items[batch_index: batch_index + TEST_BATCH_SIZE])
# load images for testing and pre-process
pre_process_params['training'] = False
images_test = putil.pre_process_batch(batch_data, pre_process_params, multi_process=True)
images_prediction = []
images_probabilities = []
for img in images_test:
print('-' * 10, 'Testing', img.id_)
start_time = timeit.default_timer()
# ##############################################################################################################
features = img.feature_matrix[0]
if NORMALIZE_FEATURES:
features = scipy_stats.zscore(features)
predictions = thegmm.predict(features)
probabilities = thegmm.predict_proba(features)
if all_probabilities is None:
all_probabilities = np.array([probabilities])
else:
all_probabilities = np.concatenate((all_probabilities, [probabilities]), axis=0)
# ##############################################################################################################
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# convert prediction and probabilities back to SimpleITK images
image_prediction = conversion.NumpySimpleITKImageBridge.convert(predictions.astype(np.uint8),
img.image_properties)
image_probabilities = conversion.NumpySimpleITKImageBridge.convert(probabilities, img.image_properties)
# evaluate segmentation without post-processing
evaluator.evaluate(image_prediction, img.images[structure.BrainImageTypes.GroundTruth], img.id_)
images_prediction.append(image_prediction)
images_probabilities.append(image_probabilities)
# post-process segmentation and evaluate with post-processing
post_process_params = {'crf_post': True}
images_post_processed = putil.post_process_batch(images_test, images_prediction, images_probabilities,
post_process_params, multi_process=True)
for i, img in enumerate(images_test):
evaluator.evaluate(images_post_processed[i], img.images[structure.BrainImageTypes.GroundTruth],
img.id_ + '-PP')
# save results
sitk.WriteImage(images_prediction[i], os.path.join(result_dir, images_test[i].id_ + '_SEG.mha'), True)
sitk.WriteImage(images_post_processed[i], os.path.join(result_dir, images_test[i].id_ + '_SEG-PP.mha'), True)
time_total_test = timeit.default_timer() - start_time_total_test
# write summary of parameters to results dir
with open(os.path.join(result_dir, 'summary.txt'), 'w') as summary_file:
print('Result dir: {}'.format(result_dir))
print('Result dir: {}'.format(result_dir), file=summary_file)
print('Training data size: {}'.format(train_data_size), file=summary_file)
print('Total training time: {:.1f}s'.format(time_total_train), file=summary_file)
print('Total testing time: {:.1f}s'.format(time_total_test), file=summary_file)
print('Voxel Filter Mask: {}'.format(putil.FeatureExtractor.VOXEL_MASK_FLT), file=summary_file)
print('Normalize Features: {}'.format(NORMALIZE_FEATURES), file=summary_file)
print('GMM', file=summary_file)
stats = statistics.gather_statistics(os.path.join(result_dir, 'results.csv'))
print('Result statistics:', file=summary_file)
print(stats, file=summary_file)
# all_probabilities.astype(np.float16).dump(os.path.join(result_dir, 'all_probabilities.npy'))
if __name__ == "__main__":
"""The program's entry point."""
script_dir = os.path.dirname(sys.argv[0])
parser = argparse.ArgumentParser(description='Medical image analysis pipeline for brain tissue segmentation')
parser.add_argument(
'--model_dir',
type=str,
default=os.path.normpath(os.path.join(script_dir, './mia-model')),
help='Base directory for output models.'
)
parser.add_argument(
'--result_dir',
type=str,
default=os.path.normpath(os.path.join(script_dir, './mia-result')),
help='Directory for results.'
)
parser.add_argument(
'--data_atlas_dir',
type=str,
default=os.path.normpath(os.path.join(script_dir, '../data/atlas')),
help='Directory with atlas data.'
)
parser.add_argument(
'--data_train_dir',
type=str,
default=os.path.normpath(os.path.join(script_dir, '../data/train/')),
help='Directory with training data.'
)
parser.add_argument(
'--data_test_dir',
type=str,
default=os.path.normpath(os.path.join(script_dir, '../data/test/')),
help='Directory with testing data.'
)
FLAGS, unparsed = parser.parse_known_args()
app.run(main=main, argv=[sys.argv[0]] + unparsed)
|
mrunibe/MIALab
|
bin/main_GMM.py
|
Python
|
apache-2.0
| 9,906
|
[
"Gaussian"
] |
1d0008f0ba2280ac08482873e48a8a1229920db29051f7da281ebe2dcd0c416b
|
# coding=utf-8
#-------------------------------------------------------------------------------
#Author: Alexandre Manhaes Savio <alexsavio@gmail.com>
#Grupo de Inteligencia Computational <www.ehu.es/ccwintco>
#Universidad del Pais Vasco UPV/EHU
#
#2013, Alexandre Manhaes Savio
#Use this at your own risk!
#-------------------------------------------------------------------------------
import os
import numpy as np
import skimage.io as skio
import matplotlib.pyplot as plt
from matplotlib import colors
import matplotlib.cm as cm
from matplotlib.widgets import Slider
import matplotlib.ticker as ticker
from mpl_toolkits.axes_grid import make_axes_locatable
from mpl_toolkits.axes_grid1 import ImageGrid
from nipy.labs.viz_tools.edge_detect import _edge_detect
from nitime.viz import drawmatrix_channels
from boyle.nifti.read import get_nii_data
from boyle.files.names import get_temp_file, remove_ext
from ..utils.math import makespread
#-------------------------------------------------------------------------------------
# Matplotlib-based options
#-------------------------------------------------------------------------------
def show_many_slices(vol, vol2=None, volaxis=1, n_slices=[8, 8], slices_idx=None,
vol1_colormap=None, vol1_transp_val=None,
vol2_colormap=None, vol2_transp_val=0,
interpolation='nearest', figtitle=None, facecolor='',
is_red_outline=False, show_colorbar=True):
"""
@param vol: numpy 3D array
@param vol2: numpy 3D array
@param volaxis: int
@param n_slices: list of int
@param slices_idx: list of int
@param vol1_colormap: matplotlib colormap
@param vol1_transp_val: vol1.dtype scalar
Volume1 transparent value
@param vol2_colormap: matplotlib colormap
@param vol2_transp_val: vol2.dtype scalar
Volume2 transparent value
@param interpolation: string, optional
@param figtitle: string, optional
@param facecolor: string, optional
@param is_red_outline: boolean, optional
@param show_colorbar: boolean, optional
@return: matplotlib figure
"""
class ImageObserver:
'update image in response to changes in clim or cmap on another image'
def __init__(self, follower):
self.follower = follower
def __call__(self, leader):
self.follower.set_cmap(leader.get_cmap())
self.follower.set_clim(leader.get_clim())
if isinstance(vol2, np.ndarray):
assert vol.shape == vol2.shape, 'vol do not have the same shape as vol2'
if vol2_colormap is None:
vol2_colormap = plt.cm.jet
if vol1_colormap is None:
vol1_colormap = plt.cm.gray
size = vol.shape[volaxis]
n_rows = len(n_slices)
n_cols = max(n_slices)
if not slices_idx:
slice_idx = makespread(list(range(size)), np.sum(n_slices))
fig = plt.figure(figtitle, frameon=False)
if facecolor:
fig.set_facecolor(facecolor)
barargs = {}
if show_colorbar:
barargs = dict(cbar_location="right",
cbar_mode='single',
cbar_size='10%',
cbar_pad=0.05)
grid = ImageGrid(fig, 111,
nrows_ncols=(n_rows, n_cols),
axes_pad=0,
direction='column',
**barargs)
axes = []
images = []
vmin = 1e40
vmax = -1e40
for g in grid:
g.axis('off')
c = 1
for i in slice_idx[:-2]:
g = grid[c-1]
img = vol.take([i], volaxis).squeeze()
if vol1_transp_val is not None:
img = np.ma.masked_where(img == vol1_transp_val, img)
g.imshow(np.rot90(img), cmap=vol1_colormap,
interpolation=interpolation)
if isinstance(vol2, np.ndarray):
img2 = vol2.take([i], volaxis).squeeze()
img2 = np.rot90(img2)
if is_red_outline:
_, img2 = _edge_detect(img2)
img2 = np.ma.masked_where(img2 == 0, img2)
#change vol2 colormap
vol2_colormap = plt.cm.autumn_r
show_colorbar = False
else:
img2 = np.ma.masked_where(img2 == vol2_transp_val, img2)
images.append(g.imshow(img2, cmap=vol2_colormap,
interpolation=interpolation))
dd = np.ravel(img2)
vmin = min(vmin, np.amin(dd))
vmax = max(vmax, np.amax(dd))
#gpos = g.get_position()
#gaxis = g.get_axis()
axes.append(g)
textx = img.shape[0]/2
texty = 4
g.text(textx, texty, str(i), horizontalalignment='center',
fontsize=12, fontname='Arial', color = '#0055ff')
c += 1
if show_colorbar:
norm = colors.Normalize(vmin=vmin, vmax=vmax)
for i, im in enumerate(images):
im.set_norm(norm)
if i > 0:
images[0].callbacksSM.connect('changed', ImageObserver(im))
axes[-1].cax.colorbar(images[-1])
return fig
def create_imglist_html(output_dir, img_files, filename='index.html'):
"""
:param img_files: list of strings
:return:
"""
#import markdown
#md_indexf = os.path.join(output_dir, 'index.markdown')
html_indexf = os.path.join(output_dir, filename)
with open(html_indexf, 'w') as f:
for imgf in img_files:
#line = '[' + imgf + '](' + imgf + ')'
#line = '[<img src="' + imgf + '" width=1000/>' + imgf + '](' + imgf + ')'
line = '<p><a href="' + imgf + '"><img src="' + imgf + '"/>' +\
imgf + '</a></p>'
f.write(line + '\n')
#markdown.markdownFromFile(md_indexf, html_indexf, encoding="utf-8")
def show_connectivity_matrix(image, cmap=None):
"""
@param image: 2D ndarray
@param cmap: colormap
"""
if cmap is None:
cmap = cm.jet
skio.imshow(image, cmap=cmap)
def autocrop_img(image, color=0):
"""
Crops the borders of the given color of an image.
@param image: ndarray
@param color: int
@return:
ndarray
"""
if len(image.shape) == 3:
img = image[..., 3] if image.shape[2] == 4 else image[..., 0]
else:
img = image
mask = (img != color).astype(int)
left, right, top, bottom = borders(mask, 0)
return image[top:bottom, left:right, :]
def imshow(image, **kwargs):
fig = plt.figure(figsize=(5, 4))
plt.imshow(image, **kwargs)
plt.axis('off')
return fig
def borders(im, color):
"""
@param im:
@param color:
@return:
"""
#left, right, top, bottom = -1,-1,-1,-1
non_color_pix = np.where(im != color)
top = non_color_pix[0].min()
bottom = non_color_pix[0].max()
left = non_color_pix[1].min()
right = non_color_pix[1].max()
return left, right, top, bottom
def slicesdir_paired_overlays(output_dir, file_list1, file_list2, dpi=150,
is_red_outline=False, **kwargs):
"""
@param output_dir:
@param file_list1: list of strings
Paths to the background image, can be either 3D or 4D images.
If they are 4D images, will pick one of the center.
@param file_list2: list of strings
Paths to the overlay images, must be 3D images.
@param is_red_outline: boolean, optional
If True will show from the files in list2 a red outline border.
@param kwargs: arguments to show_many_slices
See macuto.render.show_many_slices docstring.
@return:
"""
assert(len(file_list1) > 0)
assert(len(file_list1) == len(file_list2))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
img_files = []
#CREATE separate images of each file_list2 file
# on the corresponding file_list1 file
for idx in list(range(len(file_list1))):
f1_vol = get_nii_data(file_list1[idx])
f2_vol = get_nii_data(file_list2[idx])
if len(f1_vol.shape) > 3:
f1_vol = f1_vol[..., int(np.floor(f1_vol.shape[3]/2))]
fig = show_many_slices(f1_vol, f2_vol, is_red_outline=is_red_outline,
**kwargs)
png_fname = os.path.relpath(remove_ext(file_list1[idx]))
png_fname = png_fname.replace('.', '').replace('/', '_').replace('__', '') + '.png'
png_path = os.path.join(output_dir, png_fname)
export_figure(fig, png_path, dpi=dpi)
plt.close(fig)
img_files.append(os.path.basename(png_path))
#Create the index.html file with all images
create_imglist_html(output_dir, img_files)
return img_files
def export_figure(fig, filepath, dpi=150):
tmpf = get_temp_file(suffix='.png').name
fig.savefig(tmpf, transparent=True, dpi=dpi)
img = autocrop_img(skio.imread(tmpf))
skio.imsave(filepath, img)
return filepath
def slicesdir_oneset(output_dir, file_list1, dpi=150, **kwargs):
"""
Creates a folder with a html file and png images of slices
of each of nifti file in file_list1.
@param output_dir: string
Path to the output folder
@param file_list1: list of strings
Paths to the background image, can be either 3D or 4D images.
If they are 4D images, will pick one of the center.
@param file_list2: list of strings
Paths to the overlay images, must be 3D images.
@param kwargs: arguments to show_many_slices
See macuto.render.show_many_slices docstring.
@return:
"""
assert(len(file_list1) > 0)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
img_files = []
show_colorbar = kwargs.pop('show_colorbar', False)
#CREATE separate images of each file_list2 file
# on the corresponding file_list1 file
for idx in list(range(len(file_list1))):
f1_vol = get_nii_data(file_list1[idx])
if len(f1_vol.shape) > 3:
f1_vol = f1_vol[..., int(np.floor(f1_vol.shape[3]/2))]
fig = show_many_slices(f1_vol, show_colorbar=show_colorbar, **kwargs)
png_fname = os.path.relpath(remove_ext(file_list1[idx]))
png_fname = png_fname.replace('.', '').replace('/', '_').replace('__', '') + '.png'
png_path = os.path.join(output_dir, png_fname)
export_figure(fig, png_path, dpi=dpi)
plt.close(fig)
img_files.append(os.path.basename(png_path))
#Create the index.html file with all images
create_imglist_html(output_dir, img_files)
return img_files
def show_3slices(vol, vol2=None, x=None, y=None, z=None, fig=None,
vol2_colormap=None, vol2_transp_val=0, interpolation='nearest'):
"""
@param vol: numpy 3D array
@param vol2: numpy 3D array
@param x: int
@param y: int
@param z: int
@param fig: matplotlib Figure
@param vol2_colormap: matplotlib colormap
@param vol2_transp_val: scalar
Volume2 transparent value
@param interpolation: string
@return: matplotlib figure
"""
assert vol.shape == vol2.shape, 'vol do not have the same shape as vol2'
if not x:
x = np.floor(vol.shape[0]/2)
if not y:
y = np.floor(vol.shape[1]/2)
if not z:
z = np.floor(vol.shape[2]/2)
if not fig:
fig = plt.figure()
else:
fig = plt.figure(fig.number)
try:
if not np.ma.is_masked(vol2):
vol2 = np.ma.masked_equal(vol2, vol2_transp_val)
except:
pass
if vol2_colormap is None:
vol2_colormap = plt.cm.hot
plt.subplot (2, 2, 1)
plt.axis('off')
plt.imshow(np.rot90(vol[x, ...]), cmap=plt.cm.gray, interpolation=interpolation)
try:
plt.imshow(np.rot90(vol2[x, ...]), cmap=vol2_colormap, interpolation=interpolation)
except:
pass
#plt.imshow(vol[x,...], cmap=plt.cm.gray)
plt.title ('X:' + str(int(x)))
plt.subplot (2, 2, 2)
plt.axis('off')
plt.imshow(np.rot90(vol[:, y, :]), cmap=plt.cm.gray, interpolation=interpolation)
try:
plt.imshow(np.rot90(vol2[:, y, :]), cmap=vol2_colormap, interpolation=interpolation)
except:
pass
plt.title ('Y:' + str(int(y)))
plt.subplot (2, 2, 3)
plt.axis ('off')
plt.imshow(np.rot90(vol[..., z]), cmap=plt.cm.gray, interpolation=interpolation)
try:
plt.imshow(np.rot90(vol2[..., z]), cmap=vol2_colormap, interpolation=interpolation)
except:
pass
plt.title ('Z:' + str(int(z)))
plt.subplot (2, 2, 4)
plt.axis('off')
axcolor = 'lightgoldenrodyellow'
xval = plt.axes([0.60, 0.20, 0.20, 0.03], axisbg=axcolor)
yval = plt.axes([0.60, 0.15, 0.20, 0.03], axisbg=axcolor)
zval = plt.axes([0.60, 0.10, 0.20, 0.03], axisbg=axcolor)
xsli = Slider(xval, 'X', 0, vol.shape[0]-1, valinit=x, valfmt='%i')
ysli = Slider(yval, 'Y', 0, vol.shape[1]-1, valinit=y, valfmt='%i')
zsli = Slider(zval, 'Z', 0, vol.shape[2]-1, valinit=z, valfmt='%i')
def update(val):
x = np.around(xsli.val)
y = np.around(ysli.val)
z = np.around(zsli.val)
#debug_here()
show_3slices(vol, vol2, x, y, z, fig)
#fig.set_data()
xsli.on_changed(update)
ysli.on_changed(update)
zsli.on_changed(update)
plt.show()
return fig
def slicesdir_connectivity_matrices(output_dir, cmat_list, dpi=150,
lower_triangle=True, **kwargs):
"""
@param output_dir:
@param file_list1: list of ndarrays
List of connectivity matrices
@param dpi: int
Dots per inch resolution of the plot images
@param lower_triangle: bool
If true, will plot a lower triangle of the matrix,
the full matrix otherwise.
@param kwargs: arguments to show_many_slices
See draw_square_matrix_channels named arguments.
"""
if not os.path.exists(output_dir):
os.makedirs(output_dir)
img_files = []
#cmap = kwargs.pop('cmap', plt.cm.rainbow)
channel_names = kwargs.pop('channel_names', None)
color_anchor = kwargs.pop('color_anchor', 0)
size = kwargs.pop('size', [10., 10.])
#CREATE separate images of each file_list2 file
# on the corresponding file_list1 file
for idx in list(range(len(cmat_list))):
cmat = cmat_list[idx]
if lower_triangle:
fig = drawmatrix_channels(cmat, channel_names, size=size,
color_anchor=color_anchor, **kwargs)
else:
fig = draw_square_matrix_channels(cmat, channel_names, size=size,
color_anchor=color_anchor,
**kwargs)
png_fname = 'connectivity_matrix' + str(idx) + '.png'
png_path = os.path.join(output_dir, png_fname)
export_figure(fig, png_path, dpi=dpi)
img_files.append(os.path.basename(png_path))
plt.close()
#Create the index.html file with all images
create_imglist_html(output_dir, img_files)
return img_files
def draw_square_matrix_channels(in_m, channel_names=None, fig=None,
x_tick_rot=None, size=None, cmap=plt.cm.RdBu_r,
colorbar=True, color_anchor=None, title=None):
"""
Copied from nitime.plotting import drawmatrix_channels
Creates a full-matrix or lower-triangle of the matrix of an nxn set of values.
This is the typical format to show a symmetrical bivariate quantity (such as
correlation or coherence between two different ROIs).
@param cmat: nxn array
with values of relationships between two sets of rois or channels
@param channel_names (optional): list of strings
with the labels to be applied to the channels in the input.
Defaults to '0','1','2', etc.
@param fig (optional): a matplotlib figure
@param cmap (optional): a matplotlib colormap
to be used for displaying the values of the connections on the graph
@param title (optional): string
to title the figure (can be like '$\alpha$')
@param color_anchor (optional): int
Determine the mapping from values to colormap
if None, min and max of colormap correspond to min and max of in_m
if 0, min and max of colormap correspond to max of abs(in_m)
if (a,b), min and max of colormap correspond to (a,b)
@return: fig
a figure object
"""
N = in_m.shape[0]
ind = np.arange(N) # the evenly spaced plot indices
def channel_formatter(x):
thisind = np.clip(int(x), 0, N - 1)
return channel_names[thisind]
if fig is None:
fig = plt.figure()
if size is not None:
fig.set_figwidth(size[0])
fig.set_figheight(size[1])
w = fig.get_figwidth()
h = fig.get_figheight()
ax_im = fig.add_subplot(1, 1, 1)
#If you want to draw the colorbar:
if colorbar:
divider = make_axes_locatable(ax_im)
ax_cb = divider.new_vertical(size="10%", pad=0.1, pack_start=True)
fig.add_axes(ax_cb)
#Make a copy of the input, so that you don't make changes to the original
#data provided
m = in_m.copy()
#Extract the minimum and maximum values for scaling of the
#colormap/colorbar:
max_val = np.nanmax(m)
min_val = np.nanmin(m)
if color_anchor is None:
color_min = min_val
color_max = max_val
elif color_anchor == 0:
bound = max(abs(max_val), abs(min_val))
color_min = -bound
color_max = bound
else:
color_min = color_anchor[0]
color_max = color_anchor[1]
#The call to imshow produces the matrix plot:
im = ax_im.imshow(m, origin='upper', interpolation='nearest',
vmin=color_min, vmax=color_max, cmap=cmap)
#Formatting:
ax = ax_im
ax.grid(True)
#Label each of the cells with the row and the column:
if channel_names is not None:
if x_tick_rot is None:
if str(channel_names[0]).isdigit():
x_tick_rot = 0
else:
x_tick_rot = 45
for i in list(range(m.shape[0])):
# if i < (m.shape[0] - 1):
# ax.text(i, -1, channel_names[i],
# rotation=x_tick_rot,
# horizontalalignment='right',
# verticalalignment='bottom',
# fontsize=6)
if i > 0:
ax.text(-1, i - 1, channel_names[i],
horizontalalignment='right',
fontsize=6,
linespacing=4.)
ax.set_axis_off()
ax.set_xticks(np.arange(N))
ax.set_xticklabels(channel_names)
ax.xaxis.set_major_formatter(ticker.FuncFormatter(channel_formatter))
fig.autofmt_xdate(rotation=x_tick_rot)
ax.set_yticks(np.arange(N))
ax.set_yticklabels(channel_names)
#ax.set_ybound([-0.5, N - 0.5])
#ax.set_xbound([-0.5, N - 1.5])
#Make the tick-marks invisible:
for line in ax.xaxis.get_ticklines():
line.set_markeredgewidth(0)
for line in ax.yaxis.get_ticklines():
line.set_markeredgewidth(0)
ax.set_axis_off()
if title is not None:
ax.set_title(title)
#The following produces the colorbar and sets the ticks
if colorbar:
#Set the ticks - if 0 is in the interval of values, set that, as well
#as the maximal and minimal values:
if min_val < 0:
ticks = [color_min, min_val, 0, max_val, color_max]
#Otherwise - only set the minimal and maximal value:
else:
ticks = [color_min, min_val, max_val, color_max]
#This makes the colorbar:
cb = fig.colorbar(im, cax=ax_cb, orientation='horizontal',
cmap=cmap,
norm=im.norm,
boundaries=np.linspace(color_min, color_max, 256),
ticks=ticks,
format='%.2f')
# Set the current figure active axis to be the top-one, which is the one
# most likely to be operated on by users later on
fig.sca(ax)
return fig
#-------------------------------------------------------------------------------
# Mayavi2 options
#-------------------------------------------------------------------------------
def show_cutplanes (vol, first_idx=10, second_idx=10,
first_plane='x_axes', second_plane='y_axes'):
"""
@param vol: numpy 3d array
@param first_idx: int
@param second_idx: int
@param first_plane: string
@param second_plane: string
"""
from mayavi import mlab
mlab.pipeline.image_plane_widget(mlab.pipeline.scalar_field(vol),
plane_orientation=first_plane,
slice_index=first_idx,
colormap='gray')
mlab.pipeline.image_plane_widget(mlab.pipeline.scalar_field(vol),
plane_orientation=second_plane,
slice_index=second_idx,
colormap='gray')
mlab.outline()
def show_dynplane(vol):
"""
@param vol: numpy 3d array
"""
from mayavi import mlab
src = mlab.pipeline.scalar_field(vol)
mlab.pipeline.iso_surface(src, contours=[vol.min()+0.1*vol.ptp(), ],
opacity=0.1)
#mlab.pipeline.iso_surface(src, contours=[vol.max()-0.1*vol.ptp(), ],)
mlab.pipeline.image_plane_widget(src,
plane_orientation='z_axes',
slice_index=10,
colormap='gray')
def show_contour(vol):
"""
@param vol: numpy 3d array
"""
from mayavi import mlab
mlab.contour3d(vol, colormap='gray')
def show_render(vol, vmin=0, vmax=0.8):
"""
@param vol: numpy 3d array
@param vmin: float
@param vmax: float
"""
from mayavi import mlab
mlab.pipeline.volume(mlab.pipeline.scalar_field(vol), vmin=vmin, vmax=vmax,
colormap='gray')
|
Neurita/cajal
|
cajal/render.py
|
Python
|
bsd-3-clause
| 22,297
|
[
"Mayavi"
] |
56c8bc440867dfd1bd580566476479853b07085bd0958bd7e6b8dd08a9b02e25
|
# coding=utf-8
"""Helper functions for optimal_tree pipeline."""
from __future__ import division
import ast
from decimal import Decimal
import errno
import math
import os
import pandas
from sklearn.feature_extraction import DictVectorizer
def make_dirs(path):
"""Recursively make directories, ignoring when they already exist.
See: http://stackoverflow.com/a/600612/1275412
"""
try:
os.makedirs(path)
except OSError as exc:
if exc.errno != errno.EEXIST or not os.path.isdir(path):
raise
def _str_to_bool(s):
"""Convert string to bool (in argparse context)."""
if s.lower() not in ['true', 'false']:
raise ValueError('Need bool; got %r' % s)
return {'true': True, 'false': False}[s.lower()]
def add_boolean_argument(parser, name, default=False):
"""Add a boolean argument to an ArgumentParser instance."""
group = parser.add_mutually_exclusive_group()
group.add_argument(
'--' + name, nargs='?', default=default, const=True, type=_str_to_bool)
group.add_argument('--no' + name, dest=name, action='store_false')
# Constants
_BOLTZ = 1.3806504e-23 # # Boltzmann's constant [J/K]
_TEMP_K = 25 + 273.15 # Assumed all experiments at 25 C
_GRAV = 9.81 # Gravitational constant [m/s^2]
_PERM_FREE_SPACE = 8.854e-12 # Permittivity of vacuum. [C^2/(N.m^2)]
_ELEC_CHARGE = 1.602176466e-19 # Fundamental charge [C].
_AVOGADRO = 6.022140857e23 # Avogadro's number [1/mol]
_WATER_DIALECTRIC = 80.4 * _PERM_FREE_SPACE # Dialectric constant of water at 25C in coulombs/volt/m.
_WATER_DENSITY = 1000 * 0.9970479 # Density of water at 25C
_KINEMATIC_WATER_VISCOSITY = 8.94e-4 # Kinematic viscosity of water at 25C in Pa.s
_COLLECTOR_DENSITY = 2650 # Density of quartz sand, used as a proxy for collector [kg/m^3]
# Exponential response profile shape names.
_EXP_RP_SHAPES = ["EXP", "HE"]
# Dictionaries
# -- Electrolyte names and valences
_ELECTROLYTE_VALENCE = {
'NaCl': [1, -1],
'CaCl2': [2, -1],
'KCl': [1, -1],
'KNO3': [1, -1],
'NaHCO3': [1, -1],
'H3PO4': [1, -3],
'Na3PO4': [1, -1],
'none': [0, 0]}
# -- Electrolyte names and relative concentrations of subcomponents
_ELECTROLYTE_CONCENTRATION = {
'NaCl': [1, 1],
'CaCl2': [1, 2],
'KCl': [1, 1],
'KNO3': [1, 1],
'NaHCO3': [1, 1],
'H3PO4': [3, 1],
'Na3PO4': [3, 1],
'none': [0, 0]}
# -- ENM names and relative permittivity
_REL_PERMITTIVITIES = {
'C60': 4.4, # C60
'TiO2': 110, # TiO2
'ZnO': 2, # ZnO
'CuO': 18.1, # CuO
'MWCNTs': 1328, # MWCNTs
'Ag': 2.65, # Ag
'CeO2': 26, # CeO2
'Iron Oxide': 14.2, # Iron Oxide
# 8: 3.9, # SiO2 removed because no SiO2 with hamakers
# Originally reported at 7, but found it at 15.4 at 100Hz in Preparation and
# dielectric property of sintered monoclinic hydroxyapatite.
'nHAP': 15.4, # nHAP
# Toshiyuki Ikoma, Atsushi Yamazaki, Satoshi Nakamura, Masaru Akao
# nBiochar Dielectric properties and microwave heating of oil palm biomass
# and biochar
'nBiochar': 2.9, # biochar
# http://scholar.lib.vt.edu/theses/available/etd-04262005-181042/unrestricted/Ch2Theory.pdf
'QDs': 10.0, # CdSe
}
_BINARY_TO_RP_SHAPE_DIC = {
1: "nonexponential",
0: "exponential"
}
def electrokinetic1(row):
"""
notes: 1) zeta potentials are in mV. if in V, remove the 1e3
2) relative dialectric is for water, if this is not true,
make a column and change the function.
references:
(1) You-Im Chang and Hsun-Chih Chan.
"Correlation equation for predicting filter coefficient under
unfavorable deposition conditions".
AIChE journal, 54(5):1235–1253, 2008.
(2) Rajagopalan, R. & Kim, J. S.
"Adsorption of brownian particles in the presence of potential
barriers: effect of different modes of double-layer interaction".
Journal of Colloid and Interface Science 83, 428–448 (1981).
:param row:
:return: 1st electrokinetic parameter
"""
a = row.enm_diameter / 2 # particle radius
zp = row.enm_zeta_potential / 1e3 # particle zeta potential in V
zc = row.collector_zeta_potential / 1e3 # collector zeta potential
return _WATER_DIALECTRIC * a * (zp ** 2 + zc ** 2) / (4 * _BOLTZ * _TEMP_K)
def electrokinetic2(row):
"""
notes: 1) zeta potentials are in mV. if in V, remove the 1e3
2) relative dialectric is for water, if this is not true,
make a column and change the function.
references:
(1) You-Im Chang and Hsun-Chih Chan.
"Correlation equation for predicting filter coefficient under
unfavorable deposition conditions".
AIChE journal, 54(5):1235–1253, 2008.
(2) Rajagopalan, R. & Kim, J. S.
"Adsorption of brownian particles in the presence of potential
barriers: effect of different modes of double-layer interaction".
Journal of Colloid and Interface Science 83, 428–448 (1981).
:param row:
:return: 2nd electrokinetic parameter
"""
zp = row.enm_zeta_potential / 1e3 # particle zeta potential
zc = row.collector_zeta_potential / 1e3 # collector zeta potential
numerator = 2 * (zp / zc)
denominator = 1 + (zp / zc) ** 2
return numerator / denominator
def return_valence(row):
"""Find valence.
notes: match ENM and return valence
:param row:
:return: corresponding electrolyte valence
"""
return _ELECTROLYTE_VALENCE.get(row.electrolyte_id, [0, 0])
def electrolyte_relative_concentration(row):
"""Find relative concentration of electrolyte.
notes: match ENM and return relative concentration of ions
:param row:
:return: corresponding relative ion concentration
"""
return _ELECTROLYTE_CONCENTRATION.get(row.electrolyte_id, [0, 0])
def return_ionic_strength(row):
"""Find ionic strength.
notes: if the is an electrolyte in solution (e.g., electrolyte_rel_conc != 0),
calculate ionic strength if not, then use the pH to determine the concentration of ions in solution.
:param row:
valence:
electrolyte_rel_conc:
:return:
"""
if row.electrolyte_concentration != 0:
c_i_0 = row.electrolyte_concentration * row.electrolyte_rel_conc[0]
c_i_1 = row.electrolyte_concentration * row.electrolyte_rel_conc[1]
return 0.5 * (c_i_0 * row.valence[0] ** 2 + c_i_1 * row.valence[1] ** 2)
else:
h_plus_ions = 1.0 * 10 ** (row.ph - 14)
h_plus_valence = 1
oh_minus_ions = 1.0 * 10 ** (-1 * row.ph)
oh_minus_valence = 1
return 0.5 * (h_plus_ions * h_plus_valence ** 2) + (oh_minus_ions * oh_minus_valence ** 2)
def debye_length(row):
"""Calculate Debye length."""
numerator = _PERM_FREE_SPACE * row.enm_relative_permittivity * _BOLTZ * _TEMP_K
denominator = 2.0 * _AVOGADRO * _ELEC_CHARGE ** 2.0 * row.ionic_strength
return (numerator / denominator) ** 0.5
def edl_force(row):
"""Find EDL force.
references:
(1) Nathalie Tufenkji and Menachem Elimelech.
"Correlation Equation for Predicting Single-Collector
Efficiency in Physicochemical Filtration in Saturated
Porous Media."
Environmental Science & Technology, 38(2):529–536, January 2004
:param row:
:return: dimensionless EDL force parameter
"""
return row.enm_diameter / row.debye_length
def dim_aspect_ratio_assign(row):
"""Aspect dimensionless aspect ratio.
references:
(1) Nathalie Tufenkji and Menachem Elimelech.
"Correlation Equation for Predicting Single-Collector
Efficiency in Physicochemical Filtration in Saturated
Porous Media."
Environmental Science & Technology, 38(2):529–536, January 2004
:param row:
:return: dimensionless aspect ratio
"""
return row.enm_diameter / row.collector_diameter
def dim_peclet_num_assign(row):
"""Find Pectle number.
notes: 1) Assumes temperature of experiment is at 25C.
references:
(1) Nathalie Tufenkji and Menachem Elimelech.
"Correlation Equation for Predicting Single-Collector
Efficiency in Physicochemical Filtration in Saturated
Porous Media."
Environmental Science & Technology, 38(2):529–536, January 2004
:param row:
:return: dimensionless peclet number
"""
stokes_einstein_diffusion = _BOLTZ * _TEMP_K / (3 * math.pi * _KINEMATIC_WATER_VISCOSITY *
row.enm_diameter)
return row.darcy_velocity * row.collector_diameter / stokes_einstein_diffusion
def attraction_number(row):
"""Find attraction number.
notes: 1) Assumes temperature of experiment is at 25C.
:param row:
:return:
"""
denominator = 3.0 * math.pi * _KINEMATIC_WATER_VISCOSITY * row.enm_diameter ** 2 * row.darcy_velocity
return row.hamaker_constant_combined / denominator
def london_force(row):
"""Find London force.
notes: 1) Assumes temperature of experiment is at 25C.
references:
(1) Nathalie Tufenkji and Menachem Elimelech.
"Correlation Equation for Predicting Single-Collector
Efficiency in Physicochemical Filtration in Saturated
Porous Media."
Environmental Science & Technology, 38(2):529–536, January 2004
:param row:
:return:
"""
return row.hamaker_constant_combined / (6 * _BOLTZ * _TEMP_K)
def gravity_number(row):
"""
notes: 1) Assumes temperature of experiment is at 25C.
references:
(1) Nathalie Tufenkji and Menachem Elimelech.
"Correlation Equation for Predicting Single-Collector
Efficiency in Physicochemical Filtration in Saturated
Porous Media."
Environmental Science & Technology, 38(2):529–536, January 2004
:param row:
:return:
"""
p_radius = row.enm_diameter / 2.0
numerator = (2.0 * p_radius ** 2) * (row.enm_density - _WATER_DENSITY) * _GRAV
demoninator = 9 * _KINEMATIC_WATER_VISCOSITY * row.darcy_velocity
return numerator / demoninator
def porosity_happel(row):
"""
:param row:
:return:
"""
gam = (1 - row.porosity) ** (1 / 3)
numerator = 2 * (1 - gam ** 5)
denominator = 2 - 3 * gam + 3 * gam ** 5 - 2 * gam ** 6
return numerator / denominator
def mass_flow(row):
"""Calculate the mass flow."""
l = row.column_length
w = row.column_width
a = math.pi / 4 * row.column_width ** 2
p = row.porosity
p_vs = row.influent_pore_volumes
return l * w * a * p * p_vs
def sorbed_mass_ratio(row):
"""Find ratio of sorbed mass."""
l = row.column_length
w = row.column_width
a = math.pi / 4 * row.column_width ** 2
p = row.porosity
total_collector_mass = l * a * (1 - p) * _COLLECTOR_DENSITY
sorb_ratio = row.m_inj / total_collector_mass
return sorb_ratio
def column_aspect_ratio(row):
"""Find aspect ratio of column."""
return row.column_length / row.column_width
def binary_rp_class_assign(row):
"""Translate RP class into binary."""
if row.rp_shape in _EXP_RP_SHAPES:
return 0
else:
return 1
def binary_rp_class_assign_labels(row):
"""Assign labels based on RP class."""
if row.rp_shape in _EXP_RP_SHAPES:
return "exponential"
else:
return "nonexponential"
def rel_permittivity(row):
"""Calculate relative permittivity."""
return _REL_PERMITTIVITIES.get(row.enm_id, 10.0)
def tufenkji_eta0(row):
"""
notes: the empirical constants are derived empirically for use with CFT.
references:
(1) Nathalie Tufenkji and Menachem Elimelech.
"Correlation Equation for Predicting Single-Collector
Efficiency in Physicochemical Filtration in Saturated
Porous Media."
Environmental Science & Technology, 38(2):529–536, January 2004
:param row:
:return: returns the theoretical single collector efficiency
"""
n_dl = row.N_Dl
n_z1 = row.N_Z1
n_z2 = row.N_Z2
n_lo = row.N_Lo
n_as = row.N_as
n_r = row.N_r
n_pe = row.N_Pe
n_g = row.N_g
return (0.024 * n_dl ** (0.969) * n_z1 ** (-0.423) * n_z2 ** (2.880) * n_lo ** 1.5 +
3.176 * n_as ** (0.333) * n_r ** (-0.081) * n_pe ** (-0.715) * n_lo ** (2.687) +
0.222 * n_as * n_r ** (3.041) * n_pe ** (-0.514) * n_lo ** (0.125) +
n_r ** (-0.24) * n_g ** (1.11) * n_lo)
def rules_gradient_boost(clf, features, labels, node_index=0):
"""Structure of rules in a fit decision tree classifier
Parameters
----------
clf : DecisionTreeClassifier
A tree that has already been fit.
features, labels : lists of str
The names of the features and labels, respectively.
"""
node = {}
if clf.tree_.children_left[node_index] == -1: # indicates leaf
count_labels = zip(clf.tree_.value[node_index, 0], labels)
samples = clf.tree_.n_node_samples[node_index]
impurity = round(clf.tree_.impurity[node_index], 2)
# TODO(peterthenelson) Is it intended to ignore the label in output?
node['name'] = ', '.join('{} '.format(count)
for count, _ in count_labels)
if Decimal(node['name']) < 0:
print ast.literal_eval(node['name'])
node['name'] = '{}, nonexponential'.format(
round(Decimal(node['name']), 2)) # 'nonexponential'
else:
# node['name'] = 'exponential'
node['name'] = '{}, exponential'.format(
round(Decimal(node['name']), 2))
node['samples'] = samples
node['impurity'] = "{}".format(impurity)
# node['samples'] = ', '.join('{}'.format(samples))
else:
feature = features[clf.tree_.feature[node_index]]
threshold = '%.3E' % Decimal(clf.tree_.threshold[node_index])
samples = clf.tree_.n_node_samples[node_index]
# impurity = clf.tree_.impurity[node_index]
node['name'] = "{} >= {}".format(feature, threshold)
node['samples'] = '{}'.format(samples)
# node['impurity'] = '{}%'.format(impurity)
left_index = clf.tree_.children_left[node_index]
right_index = clf.tree_.children_right[node_index]
node['children'] = [rules(clf, features, labels, right_index),
rules(clf, features, labels, left_index)]
# print node
return node
def rules(clf, features, labels, node_index=0):
"""Structure of rules in a fit decision tree classifier.
Parameters
----------
clf : DecisionTreeClassifier
A tree that has already been fit.
features, labels : lists of str
The names of the features and labels, respectively.
"""
node = {}
if clf.tree_.children_left[node_index] == -1: # indicates leaf
count_labels = zip(clf.tree_.value[node_index, 0], labels)
samples_terminal = clf.tree_.n_node_samples[node_index]
impurity = round(clf.tree_.impurity[node_index], 3)
node['name'] = ', '.join(('{} {}'.format('%.2f' % Decimal(count), label)
for count, label in count_labels))
node['impurity'] = "{}".format(impurity)
node['samples'] = "{}".format(samples_terminal)
# print node['samples']
else:
samples = clf.tree_.n_node_samples[node_index]
feature = features[clf.tree_.feature[node_index]]
threshold = '%.3E' % Decimal(clf.tree_.threshold[node_index])
node['name'] = "{} >= {}".format(feature, threshold)
node['samples'] = '{}'.format(samples)
left_index = clf.tree_.children_left[node_index]
right_index = clf.tree_.children_right[node_index]
node['children'] = [rules(clf, features, labels, right_index),
rules(clf, features, labels, left_index)]
return node
def one_hot_dataframe(data, cols, replace=False):
"""Do hot encoding of categorical columns in a pandas DataFrame.
See:
http://scikit-learn.org/dev/modules/generated/sklearn.preprocessing.OneHotEncoder.html#sklearn.preprocessing
.OneHotEncoder
http://scikit-learn.org/dev/modules/generated/sklearn.feature_extraction.DictVectorizer.html
https://gist.github.com/kljensen/5452382
Takes a dataframe and a list of columns that need to be encoded.
Returns a 3-tuple comprising the data, the vectorized data,
and the fitted vectorizor.
"""
vec = DictVectorizer()
mkdict = lambda row: dict((col, row[col]) for col in cols)
vec_data = pandas.DataFrame(vec.fit_transform(
data[cols].apply(mkdict, axis=1)).toarray())
vec_data.columns = vec.get_feature_names()
vec_data.index = data.index
if replace is True:
data = data.drop(cols, axis=1)
data = data.join(vec_data)
return (data, vec_data, vec)
def bin_to_rp_shape(row):
"""Translate binary back to RP shape.
:param row:
:return:
"""
return _BINARY_TO_RP_SHAPE_DIC.get(row.rp_shape, "nonexponential")
|
PandaStabber/Goldberg_et_al_2016
|
helper_functions.py
|
Python
|
mit
| 17,341
|
[
"Avogadro"
] |
30af7da846590ac0c4104ab06dbb20c6c8576d47badcbde8f2b3962b276f251c
|
# -*- coding: UTF-8 -*-
"""Takes an arbitrary slice of the input data using an implicit cut
plane and warps it according to the vector field data. The scalars
are displayed on the warped surface as colors.
"""
# Authors: Fr�d�ric Petit and Prabhu Ramachandran
# Copyright (c) 2006, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Bool
from traitsui.api import View, Group, Item, InstanceEditor
from tvtk.api import tvtk
# Local imports
from mayavi.core.pipeline_info import PipelineInfo
from mayavi.core.module import Module
from mayavi.components.implicit_plane import ImplicitPlane
from mayavi.components.cutter import Cutter
from mayavi.filters.warp_vector import WarpVector
from mayavi.components.poly_data_normals import PolyDataNormals
from mayavi.components.actor import Actor
######################################################################
# `VectorCutPlane` class.
######################################################################
class WarpVectorCutPlane(Module):
# The version of this class. Used for persistence.
__version__ = 0
# The implicit plane widget used to place the implicit function.
implicit_plane = Instance(ImplicitPlane, allow_none=False,
record=True)
# The cutter. Takes a cut of the data on the implicit plane.
cutter = Instance(Cutter, allow_none=False, record=True)
# The WarpVectorCutPlane component that warps the data.
warp_vector = Instance(WarpVector, allow_none=False, record=True)
# Specify if vector normals are to be computed to make a smoother surface.
compute_normals = Bool(False, desc='if normals are to be computed '\
'to make the warped surface smoother')
# The component that computes the normals.
normals = Instance(PolyDataNormals, record=True)
# The Actor component.
actor = Instance(Actor, allow_none=False, record=True)
input_info = PipelineInfo(datasets=['any'],
attribute_types=['any'],
attributes=['vectors'])
########################################
# View related traits.
_warp_group = Group(Item(name='filter',
style='custom',
editor=\
InstanceEditor(view=
View(Item('scale_factor')))),
show_labels=False)
view = View(Group(Item(name='implicit_plane', style='custom'),
label='ImplicitPlane',
show_labels=False),
Group(Group(Item(name='warp_vector',
style='custom',
resizable=True,
show_label=False,
editor=InstanceEditor(view=View(_warp_group))
),
),
Item(name='_'),
Item(name='compute_normals'),
Group(Item(name='normals',
style='custom',
show_label=False,
enabled_when = 'compute_normals'),
),
label='WarpVector',
show_labels=True),
Group(Item(name='actor', style='custom'),
label='Actor',
show_labels=False),
resizable=True,
)
######################################################################
# `Module` interface
######################################################################
def setup_pipeline(self):
"""Override this method so that it *creates* the tvtk
pipeline.
This method is invoked when the object is initialized via
`__init__`. Note that at the time this method is called, the
tvtk data pipeline will *not* yet be setup. So upstream data
will not be available. The idea is that you simply create the
basic objects and setup those parts of the pipeline not
dependent on upstream sources and filters. You should also
set the `actors` attribute up at this point.
"""
# Create the objects and set them up.
self.implicit_plane = ImplicitPlane()
self.cutter = Cutter()
self.warp_vector = WarpVector()
self.normals = PolyDataNormals()
actor = self.actor = Actor()
actor.mapper.scalar_visibility = 1
def update_pipeline(self):
"""Override this method so that it *updates* the tvtk pipeline
when data upstream is known to have changed.
This method is invoked (automatically) when any of the inputs
sends a `pipeline_changed` event.
"""
mm = self.module_manager
if mm is None:
return
self.implicit_plane.inputs = [mm.source]
# Force the vector normals setting to be noted.
self._compute_normals_changed(self.compute_normals)
# Set the LUT for the mapper.
self.actor.set_lut(mm.scalar_lut_manager.lut)
self.pipeline_changed = True
def update_data(self):
"""Override this method so that it flushes the vtk pipeline if
that is necessary.
This method is invoked (automatically) when any of the inputs
sends a `data_changed` event.
"""
# Just set data_changed, the other components should do the rest.
self.data_changed = True
######################################################################
# Non-public traits.
######################################################################
def _compute_normals_changed(self, value):
if self.module_manager is None:
return
actor = self.actor
if actor is not None:
if value:
actor.inputs = [self.normals]
else:
actor.inputs = [self.warp_vector]
self.render()
def _normals_changed(self, old, new):
warp_vector = self.warp_vector
compute_normals = self.compute_normals
if compute_normals is not None:
new.inputs = [warp_vector]
self._compute_normals_changed(self.compute_normals)
self._change_components(old, new)
def _implicit_plane_changed(self, old, new):
cutter = self.cutter
if cutter is not None:
cutter.cut_function = new.plane
cutter.inputs = [new]
self._change_components(old, new)
def _warp_vector_changed(self, old, new):
cutter = self.cutter
if cutter is not None:
new.inputs = [cutter]
self._compute_normals_changed(self.compute_normals)
self._change_components(old, new)
def _cutter_changed(self, old, new):
ip = self.implicit_plane
if ip is not None:
new.cut_function = ip.plane
new.inputs = [ip]
w = self.warp_vector
if w is not None:
w.inputs = [new]
self._change_components(old, new)
def _actor_changed(self, old, new):
self._compute_normals_changed(self.compute_normals)
self._change_components(old, new)
|
dmsurti/mayavi
|
mayavi/modules/warp_vector_cut_plane.py
|
Python
|
bsd-3-clause
| 7,380
|
[
"Mayavi",
"VTK"
] |
66d1ddf6787916ab1c6896b4605be53b20ac7249eab1380a1e6860e0112b07d2
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Ansible. If not, see <http://www.gnu.org/licenses/>.
DOCUMENTATION = '''
module: systemd
author:
- "Ansible Core Team"
version_added: "2.2"
short_description: Manage services.
description:
- Controls systemd services on remote hosts.
options:
name:
required: true
description:
- Name of the service.
aliases: ['unit', 'service']
state:
required: false
default: null
choices: [ 'started', 'stopped', 'restarted', 'reloaded' ]
description:
- C(started)/C(stopped) are idempotent actions that will not run commands unless necessary.
C(restarted) will always bounce the service. C(reloaded) will always reload.
enabled:
required: false
choices: [ "yes", "no" ]
default: null
description:
- Whether the service should start on boot. B(At least one of state and enabled are required.)
masked:
required: false
choices: [ "yes", "no" ]
default: null
description:
- Whether the unit should be masked or not, a masked unit is impossible to start.
daemon_reload:
required: false
default: no
choices: [ "yes", "no" ]
description:
- run daemon-reload before doing any other operations, to make sure systemd has read any changes.
aliases: ['daemon-reload']
user:
required: false
default: no
choices: [ "yes", "no" ]
description:
- run systemctl talking to the service manager of the calling user, rather than the service manager
of the system.
notes:
- One option other than name is required.
requirements:
- A system managed by systemd
'''
EXAMPLES = '''
# Example action to start service httpd, if not running
- systemd: state=started name=httpd
# Example action to stop service cron on debian, if running
- systemd: name=cron state=stopped
# Example action to restart service cron on centos, in all cases, also issue daemon-reload to pick up config changes
- systemd:
state: restarted
daemon_reload: yes
name: crond
# Example action to reload service httpd, in all cases
- systemd:
name: httpd
state: reloaded
# Example action to enable service httpd and ensure it is not masked
- systemd:
name: httpd
enabled: yes
masked: no
# Example action to enable a timer for dnf-automatic
- systemd:
name: dnf-automatic.timer
state: started
enabled: True
'''
RETURN = '''
status:
description: A dictionary with the key=value pairs returned from `systemctl show`
returned: success
type: complex
sample: {
"ActiveEnterTimestamp": "Sun 2016-05-15 18:28:49 EDT",
"ActiveEnterTimestampMonotonic": "8135942",
"ActiveExitTimestampMonotonic": "0",
"ActiveState": "active",
"After": "auditd.service systemd-user-sessions.service time-sync.target systemd-journald.socket basic.target system.slice",
"AllowIsolate": "no",
"Before": "shutdown.target multi-user.target",
"BlockIOAccounting": "no",
"BlockIOWeight": "1000",
"CPUAccounting": "no",
"CPUSchedulingPolicy": "0",
"CPUSchedulingPriority": "0",
"CPUSchedulingResetOnFork": "no",
"CPUShares": "1024",
"CanIsolate": "no",
"CanReload": "yes",
"CanStart": "yes",
"CanStop": "yes",
"CapabilityBoundingSet": "18446744073709551615",
"ConditionResult": "yes",
"ConditionTimestamp": "Sun 2016-05-15 18:28:49 EDT",
"ConditionTimestampMonotonic": "7902742",
"Conflicts": "shutdown.target",
"ControlGroup": "/system.slice/crond.service",
"ControlPID": "0",
"DefaultDependencies": "yes",
"Delegate": "no",
"Description": "Command Scheduler",
"DevicePolicy": "auto",
"EnvironmentFile": "/etc/sysconfig/crond (ignore_errors=no)",
"ExecMainCode": "0",
"ExecMainExitTimestampMonotonic": "0",
"ExecMainPID": "595",
"ExecMainStartTimestamp": "Sun 2016-05-15 18:28:49 EDT",
"ExecMainStartTimestampMonotonic": "8134990",
"ExecMainStatus": "0",
"ExecReload": "{ path=/bin/kill ; argv[]=/bin/kill -HUP $MAINPID ; ignore_errors=no ; start_time=[n/a] ; stop_time=[n/a] ; pid=0 ; code=(null) ; status=0/0 }",
"ExecStart": "{ path=/usr/sbin/crond ; argv[]=/usr/sbin/crond -n $CRONDARGS ; ignore_errors=no ; start_time=[n/a] ; stop_time=[n/a] ; pid=0 ; code=(null) ; status=0/0 }",
"FragmentPath": "/usr/lib/systemd/system/crond.service",
"GuessMainPID": "yes",
"IOScheduling": "0",
"Id": "crond.service",
"IgnoreOnIsolate": "no",
"IgnoreOnSnapshot": "no",
"IgnoreSIGPIPE": "yes",
"InactiveEnterTimestampMonotonic": "0",
"InactiveExitTimestamp": "Sun 2016-05-15 18:28:49 EDT",
"InactiveExitTimestampMonotonic": "8135942",
"JobTimeoutUSec": "0",
"KillMode": "process",
"KillSignal": "15",
"LimitAS": "18446744073709551615",
"LimitCORE": "18446744073709551615",
"LimitCPU": "18446744073709551615",
"LimitDATA": "18446744073709551615",
"LimitFSIZE": "18446744073709551615",
"LimitLOCKS": "18446744073709551615",
"LimitMEMLOCK": "65536",
"LimitMSGQUEUE": "819200",
"LimitNICE": "0",
"LimitNOFILE": "4096",
"LimitNPROC": "3902",
"LimitRSS": "18446744073709551615",
"LimitRTPRIO": "0",
"LimitRTTIME": "18446744073709551615",
"LimitSIGPENDING": "3902",
"LimitSTACK": "18446744073709551615",
"LoadState": "loaded",
"MainPID": "595",
"MemoryAccounting": "no",
"MemoryLimit": "18446744073709551615",
"MountFlags": "0",
"Names": "crond.service",
"NeedDaemonReload": "no",
"Nice": "0",
"NoNewPrivileges": "no",
"NonBlocking": "no",
"NotifyAccess": "none",
"OOMScoreAdjust": "0",
"OnFailureIsolate": "no",
"PermissionsStartOnly": "no",
"PrivateNetwork": "no",
"PrivateTmp": "no",
"RefuseManualStart": "no",
"RefuseManualStop": "no",
"RemainAfterExit": "no",
"Requires": "basic.target",
"Restart": "no",
"RestartUSec": "100ms",
"Result": "success",
"RootDirectoryStartOnly": "no",
"SameProcessGroup": "no",
"SecureBits": "0",
"SendSIGHUP": "no",
"SendSIGKILL": "yes",
"Slice": "system.slice",
"StandardError": "inherit",
"StandardInput": "null",
"StandardOutput": "journal",
"StartLimitAction": "none",
"StartLimitBurst": "5",
"StartLimitInterval": "10000000",
"StatusErrno": "0",
"StopWhenUnneeded": "no",
"SubState": "running",
"SyslogLevelPrefix": "yes",
"SyslogPriority": "30",
"TTYReset": "no",
"TTYVHangup": "no",
"TTYVTDisallocate": "no",
"TimeoutStartUSec": "1min 30s",
"TimeoutStopUSec": "1min 30s",
"TimerSlackNSec": "50000",
"Transient": "no",
"Type": "simple",
"UMask": "0022",
"UnitFileState": "enabled",
"WantedBy": "multi-user.target",
"Wants": "system.slice",
"WatchdogTimestampMonotonic": "0",
"WatchdogUSec": "0",
}
'''
from ansible.module_utils.basic import AnsibleModule
from ansible.module_utils.service import sysv_exists, sysv_is_enabled, fail_if_missing
from ansible.module_utils._text import to_native
# ===========================================
# Main control flow
def main():
# initialize
module = AnsibleModule(
argument_spec = dict(
name = dict(required=True, type='str', aliases=['unit', 'service']),
state = dict(choices=[ 'started', 'stopped', 'restarted', 'reloaded'], type='str'),
enabled = dict(type='bool'),
masked = dict(type='bool'),
daemon_reload= dict(type='bool', default=False, aliases=['daemon-reload']),
user= dict(type='bool', default=False),
),
supports_check_mode=True,
required_one_of=[['state', 'enabled', 'masked', 'daemon_reload']],
)
systemctl = module.get_bin_path('systemctl')
if module.params['user']:
systemctl = systemctl + " --user"
unit = module.params['name']
rc = 0
out = err = ''
result = {
'name': unit,
'changed': False,
'status': {},
'warnings': [],
}
# Run daemon-reload first, if requested
if module.params['daemon_reload']:
(rc, out, err) = module.run_command("%s daemon-reload" % (systemctl))
if rc != 0:
module.fail_json(msg='failure %d during daemon-reload: %s' % (rc, err))
found = False
is_initd = sysv_exists(unit)
is_systemd = False
# check service data, cannot error out on rc as it changes across versions, assume not found
(rc, out, err) = module.run_command("%s show '%s'" % (systemctl, unit))
if rc == 0:
# load return of systemctl show into dictionary for easy access and return
multival = []
if out:
k = None
for line in to_native(out).split('\n'): # systemd can have multiline values delimited with {}
if line.strip():
if k is None:
if '=' in line:
k,v = line.split('=', 1)
if v.lstrip().startswith('{'):
if not v.rstrip().endswith('}'):
multival.append(line)
continue
result['status'][k] = v.strip()
k = None
else:
if line.rstrip().endswith('}'):
result['status'][k] = '\n'.join(multival).strip()
multival = []
k = None
else:
multival.append(line)
is_systemd = 'LoadState' in result['status'] and result['status']['LoadState'] != 'not-found'
# Check for loading error
if is_systemd and 'LoadError' in result['status']:
module.fail_json(msg="Error loading unit file '%s': %s" % (unit, result['status']['LoadError']))
# Does service exist?
found = is_systemd or is_initd
if is_initd and not is_systemd:
result['warnings'].append('The service (%s) is actually an init script but the system is managed by systemd' % unit)
# mask/unmask the service, if requested, can operate on services before they are installed
if module.params['masked'] is not None:
# state is not masked unless systemd affirms otherwise
masked = ('LoadState' in result['status'] and result['status']['LoadState'] == 'masked')
if masked != module.params['masked']:
result['changed'] = True
if module.params['masked']:
action = 'mask'
else:
action = 'unmask'
if not module.check_mode:
(rc, out, err) = module.run_command("%s %s '%s'" % (systemctl, action, unit))
if rc != 0:
# some versions of system CAN mask/unmask non existing services, we only fail on missing if they don't
fail_if_missing(module, found, unit, msg='host')
# Enable/disable service startup at boot if requested
if module.params['enabled'] is not None:
if module.params['enabled']:
action = 'enable'
else:
action = 'disable'
fail_if_missing(module, found, unit, msg='host')
# do we need to enable the service?
enabled = False
(rc, out, err) = module.run_command("%s is-enabled '%s'" % (systemctl, unit))
# check systemctl result or if it is a init script
if rc == 0:
enabled = True
elif rc == 1:
# if both init script and unit file exist stdout should have enabled/disabled, otherwise use rc entries
if is_initd and (not out.startswith('disabled') or sysv_is_enabled(unit)):
enabled = True
# default to current state
result['enabled'] = enabled
# Change enable/disable if needed
if enabled != module.params['enabled']:
result['changed'] = True
if not module.check_mode:
(rc, out, err) = module.run_command("%s %s '%s'" % (systemctl, action, unit))
if rc != 0:
module.fail_json(msg="Unable to %s service %s: %s" % (action, unit, out + err))
result['enabled'] = not enabled
# set service state if requested
if module.params['state'] is not None:
fail_if_missing(module, found, unit, msg="host")
# default to desired state
result['state'] = module.params['state']
# What is current service state?
if 'ActiveState' in result['status']:
action = None
if module.params['state'] == 'started':
if result['status']['ActiveState'] != 'active':
action = 'start'
elif module.params['state'] == 'stopped':
if result['status']['ActiveState'] == 'active':
action = 'stop'
else:
action = module.params['state'][:-2] # remove 'ed' from restarted/reloaded
result['state'] = 'started'
if action:
result['changed'] = True
if not module.check_mode:
(rc, out, err) = module.run_command("%s %s '%s'" % (systemctl, action, unit))
if rc != 0:
module.fail_json(msg="Unable to %s service %s: %s" % (action, unit, err))
else:
# this should not happen?
module.fail_json(msg="Service is in unknown state", status=result['status'])
module.exit_json(**result)
if __name__ == '__main__':
main()
|
dmillington/ansible-modules-core
|
system/systemd.py
|
Python
|
gpl-3.0
| 15,510
|
[
"Brian"
] |
3c2785c54729cb9049fd8ade0838fda4830549cf10723f21f605a35d41f8b3f1
|
"""
Job Base Class
This class provides generic job definition functionality suitable for any VO.
Helper functions are documented with example usage for the DIRAC API. An example
script (for a simple executable) would be::
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.Interfaces.API.Job import Job
j = Job()
j.setCPUTime(500)
j.setExecutable('/bin/echo hello')
j.setExecutable('yourPythonScript.py')
j.setExecutable('/bin/echo hello again')
j.setName('MyJobName')
dirac = Dirac()
jobID = dirac.submit(j)
print 'Submission Result: ',jobID
Note that several executables can be provided and wil be executed sequentially.
"""
__RCSID__ = "$Id$"
import re, os, types, urllib
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Workflow.Parameter import Parameter
from DIRAC.Core.Workflow.Workflow import Workflow
from DIRAC.Core.Base.API import API
from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
from DIRAC.ConfigurationSystem.Client.Config import gConfig
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOForGroup
from DIRAC.Core.Utilities.Subprocess import shellCall
from DIRAC.Core.Utilities.List import uniqueElements
from DIRAC.Core.Utilities.SiteCEMapping import getSiteForCE, getSiteCEMapping
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.ConfigurationSystem.Client.Helpers import Resources
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.Workflow.Utilities.Utils import getStepDefinition, addStepToWorkflow
COMPONENT_NAME = '/Interfaces/API/Job'
class Job( API ):
""" DIRAC jobs
"""
#############################################################################
def __init__( self, script = None, stdout = 'std.out', stderr = 'std.err' ):
"""Instantiates the Workflow object and some default parameters.
"""
super( Job, self ).__init__()
self.dbg = False
if gConfig.getValue( self.section + '/LogLevel', 'DEBUG' ) == 'DEBUG':
self.dbg = True
#gConfig.getValue('Tier0SE-tape','SEName')
self.stepCount = 0
self.owner = 'NotSpecified'
self.name = 'Name'
self.type = 'User'
self.priority = 1
vo = ''
ret = getProxyInfo( disableVOMS = True )
if ret['OK'] and 'group' in ret['Value']:
vo = getVOForGroup( ret['Value']['group'] )
self.group = vo
self.site = 'ANY' #ANY
#self.setup = 'Development'
self.origin = 'DIRAC'
self.stdout = stdout
self.stderr = stderr
self.logLevel = 'info'
self.executable = '$DIRACROOT/scripts/dirac-jobexec' # to be clarified
self.addToInputSandbox = []
self.addToOutputSandbox = []
self.addToInputData = []
##Add member to handle Parametric jobs
self.parametric = {}
self.script = script
if not script:
self.workflow = Workflow()
self.__setJobDefaults()
else:
self.workflow = Workflow( script )
#############################################################################
def setExecutable( self, executable, arguments = '', logFile = '',
modulesList = ['Script'],
parameters = [( 'executable', 'string', '', "Executable Script" ),
( 'arguments', 'string', '', 'Arguments for executable Script' ),
( 'applicationLog', 'string', '', "Log file name" )],
paramValues = [] ):
"""Helper function.
Specify executable script to run with optional arguments and log file
for standard output.
These can be either:
- Submission of a python or shell script to DIRAC
- Can be inline scripts e.g. C{'/bin/ls'}
- Scripts as executables e.g. python or shell script file
Example usage:
>>> job = Job()
>>> job.setExecutable('myScript.py')
@param executable: Executable
@type executable: string
@param arguments: Optional arguments to executable
@type arguments: string
@param logFile: Optional log file name
@type logFile: string
@param modulesList: Optional list of modules (to be used mostly when extending this method)
@type modulesList: list
@param parameters: Optional list of parameters (to be used mostly when extending this method)
@type parameters: list of tuples
@param paramValues: Optional list of parameters values (to be used mostly when extending this method)
@type parameters: list of tuples
"""
kwargs = {'executable':executable, 'arguments':arguments, 'logFile':logFile}
if not type( executable ) == type( ' ' ) or not type( arguments ) == type( ' ' ) or \
not type( logFile ) == type( ' ' ):
return self._reportError( 'Expected strings for executable and arguments', **kwargs )
if os.path.exists( executable ):
self.log.verbose( 'Found script executable file %s' % ( executable ) )
self.addToInputSandbox.append( executable )
logName = '%s.log' % ( os.path.basename( executable ) )
else:
self.log.warn( 'The executable code could not be found locally' )
logName = 'CodeOutput.log'
self.stepCount += 1
stepName = 'RunScriptStep%s' % ( self.stepCount )
if logFile:
if type( logFile ) == type( ' ' ):
logName = str(logFile)
else:
logName = "Script%s_%s" %( self.stepCount, logName )
step = getStepDefinition( 'ScriptStep%s' % ( self.stepCount ), modulesList, parametersList = parameters )
self.addToOutputSandbox.append( logName )
stepInstance = addStepToWorkflow( self.workflow, step, stepName )
stepInstance.setValue( 'applicationLog', logName )
stepInstance.setValue( 'executable', executable )
if arguments:
stepInstance.setValue( 'arguments', arguments )
if paramValues:
for param, value in paramValues:
stepInstance.setValue( param, value )
return S_OK( stepInstance )
#############################################################################
def setName( self, jobName ):
"""Helper function.
A name for the job can be specified if desired. This will appear
in the JobName field of the monitoring webpage. If nothing is
specified a default value will appear.
Example usage:
>>> job=Job()
>>> job.setName("myJobName")
:param jobName: Name of job
:type jobName: string
"""
kwargs = {'jobname':jobName}
if not type( jobName ) == type( ' ' ):
return self._reportError( 'Expected strings for job name', **kwargs )
else:
self.workflow.setName( jobName )
self._addParameter( self.workflow, 'JobName', 'JDL', jobName, 'User specified name' )
return S_OK()
#############################################################################
def setInputSandbox( self, files ):
"""Helper function.
Specify input sandbox files less than 10MB in size. If over 10MB, files
or a directory may be uploaded to Grid storage, see C{dirac.uploadSandbox()}.
Paths to the options file and (if required) 'lib/' directory of the DLLs
are specified here. Default is local directory. CMT requirements files or
executables may be placed in the lib/ directory if desired. The lib/ directory
is transferred to the Grid Worker Node before the job executes.
Files / directories can be specified using the `*` character e.g. `*.txt` these
are resolved correctly before job execution on the WN.
Example usage:
>>> job = Job()
>>> job.setInputSandbox(['DaVinci.opts'])
:param files: Input sandbox files, can specify full path
:type files: Single string or list of strings ['','']
"""
if type( files ) == list and len( files ):
resolvedFiles = self._resolveInputSandbox( files )
fileList = ';'.join( resolvedFiles )
description = 'Input sandbox file list'
self._addParameter( self.workflow, 'InputSandbox', 'JDL', fileList, description )
#self.sandboxFiles=resolvedFiles
elif type( files ) == type( " " ):
resolvedFiles = self._resolveInputSandbox( [files] )
fileList = ';'.join( resolvedFiles )
description = 'Input sandbox file'
#self.sandboxFiles = [files]
self._addParameter( self.workflow, 'InputSandbox', 'JDL', fileList, description )
else:
kwargs = {'files':files}
return self._reportError( 'Expected file string or list of files for input sandbox contents', **kwargs )
return S_OK()
#############################################################################
def setParametricInputSandbox( self, files ):
"""Helper function.
Specify input sandbox files to used as parameters in the Parametric jobs. The possibilities are identical to the setInputSandbox.
Example usage:
>>> job = Job()
>>> job.setParametricInputSandbox(['LFN:/Some_file','LFN:/Some_other_file'])
:param files: Logical File Names
:type files: Single LFN string or list of LFNs
"""
kwargs = {'files':files}
if type( files ) == list and len( files ):
for fileName in files:
if not fileName.lower().count( "lfn:" ):
return self._reportError( 'All files should be LFNs', **kwargs )
resolvedFiles = self._resolveInputSandbox( files )
self.parametric['InputSandbox'] = resolvedFiles
#self.sandboxFiles=resolvedFiles
elif type( files ) == type( " " ):
if not files.lower().count( "lfn:" ):
return self._reportError( 'All files should be LFNs', **kwargs )
resolvedFiles = self._resolveInputSandbox( [files] )
self.parametric['InputSandbox'] = resolvedFiles
#self.sandboxFiles = [files]
else:
return self._reportError( 'Expected file string or list of files for input sandbox contents', **kwargs )
return S_OK()
#############################################################################
def setOutputSandbox( self, files ):
"""Helper function.
Specify output sandbox files. If specified files are over 10MB, these
may be uploaded to Grid storage with a notification returned in the
output sandbox.
Example usage:
>>> job = Job()
>>> job.setOutputSandbox(['DaVinci_v19r12.log','DVNTuples.root'])
:param files: Output sandbox files
:type files: Single string or list of strings ['','']
"""
if type( files ) == list and len( files ):
fileList = ';'.join( files )
description = 'Output sandbox file list'
self._addParameter( self.workflow, 'OutputSandbox', 'JDL', fileList, description )
elif type( files ) == type( " " ):
description = 'Output sandbox file'
self._addParameter( self.workflow, 'OutputSandbox', 'JDL', files, description )
else:
kwargs = {'files':files}
return self._reportError( 'Expected file string or list of files for output sandbox contents', **kwargs )
return S_OK()
#############################################################################
def setInputData( self, lfns ):
"""Helper function.
Specify input data by Logical File Name (LFN).
Example usage:
>>> job = Job()
>>> job.setInputData(['/lhcb/production/DC04/v2/DST/00000742_00003493_10.dst'])
:param lfns: Logical File Names
:type lfns: Single LFN string or list of LFNs
"""
if type( lfns ) == list and len( lfns ):
for i in xrange( len( lfns ) ):
lfns[i] = lfns[i].replace( 'LFN:', '' )
inputData = ['LFN:' + x for x in lfns ]
inputDataStr = ';'.join( inputData )
description = 'List of input data specified by LFNs'
self._addParameter( self.workflow, 'InputData', 'JDL', inputDataStr, description )
elif type( lfns ) == type( ' ' ): #single LFN
description = 'Input data specified by LFN'
self._addParameter( self.workflow, 'InputData', 'JDL', lfns, description )
else:
kwargs = {'lfns':lfns}
return self._reportError( 'Expected lfn string or list of lfns for input data', **kwargs )
return S_OK()
#############################################################################
def setParametricInputData( self, lfns ):
"""Helper function.
Specify input data by Logical File Name (LFN) to be used as a parameter in a parametric job
Example usage:
>>> job = Job()
>>> job.setParametricInputData(['/lhcb/production/DC04/v2/DST/00000742_00003493_10.dst'])
:param lfns: Logical File Names
:type lfns: Single LFN string or list of LFNs
"""
if type( lfns ) == list and len( lfns ):
for i in xrange( len( lfns ) ):
if type( lfns[i] ) == list and len( lfns[i] ):
for k in xrange( len( lfns[i] ) ):
lfns[i][k] = 'LFN:' + lfns[i][k].replace( 'LFN:', '' )
else:
lfns[i] = 'LFN:' + lfns[i].replace( 'LFN:', '' )
self.parametric['InputData'] = lfns
elif type( lfns ) == type( ' ' ): #single LFN
self.parametric['InputData'] = lfns
else:
kwargs = {'lfns':lfns}
return self._reportError( 'Expected lfn string or list of lfns for parametric input data', **kwargs )
return S_OK()
#############################################################################
def setGenericParametricInput( self, inputlist ):
""" Helper function
Define a generic parametric job with this function. Should not be used when
the ParametricInputData of ParametricInputSandbox are used.
:param inputlist: Input list of parameters to build the parametric job
:type inputlist: list
"""
kwargs = {'inputlist':inputlist}
if not type( inputlist ) == type( [] ):
return self._reportError( 'Expected list for parameters', **kwargs )
self.parametric['GenericParameters'] = inputlist
return S_OK()
#############################################################################
def setInputDataPolicy( self, policy, dataScheduling = True ):
"""Helper function.
Specify a job input data policy, this takes precedence over any site specific or
global settings.
Possible values for policy are 'Download' or 'Protocol' (case-insensitive). This
requires that the module locations are defined for the VO in the CS.
Example usage:
>>> job = Job()
>>> job.setInputDataPolicy('download')
"""
kwargs = {'policy':policy, 'dataScheduling':dataScheduling}
csSection = 'InputDataPolicy'
possible = ['Download', 'Protocol']
finalPolicy = ''
for value in possible:
if policy.lower() == value.lower():
finalPolicy = value
if not finalPolicy:
return self._reportError( 'Expected one of %s for input data policy' % ( ', '.join( possible ) ),
__name__, **kwargs )
jobPolicy = Operations().getValue( '%s/%s' % ( csSection, finalPolicy ), '' )
if not jobPolicy:
return self._reportError( 'Could not get value for Operations option %s/%s' % ( csSection, finalPolicy ),
__name__, **kwargs )
description = 'User specified input data policy'
self._addParameter( self.workflow, 'InputDataPolicy', 'JDL', jobPolicy, description )
if not dataScheduling and policy.lower() == 'download':
self.log.verbose( 'Scheduling by input data is disabled, jobs will run anywhere and download input data' )
self._addParameter( self.workflow, 'DisableDataScheduling', 'JDL', 'True', 'Disable scheduling by input data' )
if not dataScheduling and policy.lower() != 'download':
self.log.error( 'Expected policy to be "download" for bypassing data scheduling' )
return self._reportError( 'Expected policy to be "download" for bypassing data scheduling',
__name__, **kwargs )
return S_OK()
#############################################################################
def setOutputData( self, lfns, outputSE = None, outputPath = '' ):
"""Helper function.
For specifying output data to be registered in Grid storage. If a list
of OutputSEs are specified the job wrapper will try each in turn until
successful. If the OutputPath is specified this will appear only after
/ <VO> / user / <initial> / <username>
directory.
Example usage:
>>> job = Job()
>>> job.setOutputData(['DVNtuple.root'])
:param lfns: Output data file or files
:type lfns: Single string or list of strings ['','']
:param outputSE: Optional parameter to specify the Storage Element
:param outputPath: Optional parameter to specify part of the path in the storage (see above)
Element to store data or files, e.g. CERN-tape
:type outputSE: string or list
:type outputPath: string
"""
if outputSE == None:
outputSE = []
kwargs = {'lfns':lfns, 'OutputSE':outputSE, 'OutputPath':outputPath}
if type( lfns ) == list and len( lfns ):
outputDataStr = ';'.join( lfns )
description = 'List of output data files'
self._addParameter( self.workflow, 'OutputData', 'JDL', outputDataStr, description )
elif type( lfns ) == type( " " ):
description = 'Output data file'
self._addParameter( self.workflow, 'OutputData', 'JDL', lfns, description )
else:
return self._reportError( 'Expected file name string or list of file names for output data', **kwargs )
if outputSE:
description = 'User specified Output SE'
if type( outputSE ) in types.StringTypes:
outputSE = [outputSE]
elif type( outputSE ) != types.ListType:
return self._reportError( 'Expected string or list for OutputSE', **kwargs )
outputSE = ';'.join( outputSE )
self._addParameter( self.workflow, 'OutputSE', 'JDL', outputSE, description )
if outputPath:
description = 'User specified Output Path'
if not type( outputPath ) in types.StringTypes:
return self._reportError( 'Expected string for OutputPath', **kwargs )
# Remove leading "/" that might cause problems with os.path.join
# FIXME: this will prevent to set OutputPath outside the Home of the User
while outputPath[0] == '/':
outputPath = outputPath[1:]
self._addParameter( self.workflow, 'OutputPath', 'JDL', outputPath, description )
return S_OK()
#############################################################################
def setPlatform( self, platform ):
"""Developer function: sets the target platform, e.g. Linux_x86_64_glibc-2.5.
This platform is in the form of what it is returned by the dirac-platform script
(or dirac-architecture if your extension provides it)
"""
kwargs = {'platform':platform}
if not type( platform ) == type( " " ):
return self._reportError( "Expected string for platform", **kwargs )
if not platform.lower() == 'any':
availablePlatforms = Resources.getDIRACPlatforms()
if not availablePlatforms['OK']:
return self._reportError( "Can't check for platform", **kwargs )
if platform in availablePlatforms['Value']:
self._addParameter( self.workflow, 'Platform', 'JDL', platform, 'Platform ( Operating System )' )
else:
return self._reportError( "Invalid platform", **kwargs )
return S_OK()
#############################################################################
def setSubmitPool( self, backend ):
"""Developer function.
Choose submission pool on which job is executed.
Default in place for users.
"""
#should add protection here for list of supported platforms
kwargs = {'backend':backend}
if not type( backend ) in types.StringTypes:
return self._reportError( 'Expected string for SubmitPool', **kwargs )
if not backend.lower() == 'any':
self._addParameter( self.workflow, 'SubmitPools', 'JDL', backend, 'Submit Pool' )
return S_OK()
#############################################################################
def setCPUTime( self, timeInSecs ):
"""Helper function.
Under Development. Specify CPU time requirement in DIRAC units.
Example usage:
>>> job = Job()
>>> job.setCPUTime(5000)
:param timeInSecs: CPU time
:type timeInSecs: Int
"""
kwargs = {'timeInSecs':timeInSecs}
if not type( timeInSecs ) == int:
try:
timeInSecs = int( timeInSecs )
except Exception:
if not re.search( '{{', timeInSecs ):
return self._reportError( 'Expected numerical string or int for CPU time in seconds', **kwargs )
description = 'CPU time in secs'
self._addParameter( self.workflow, 'MaxCPUTime', 'JDL', timeInSecs, description )
return S_OK()
#############################################################################
def setDestination( self, destination ):
"""Helper function.
Can specify a desired destination site or sites for job. This can be useful
for debugging purposes but often limits the possible candidate sites
and overall system response time.
Example usage:
>>> job = Job()
>>> job.setDestination('LCG.CERN.ch')
:param destination: site string
:type destination: string or list
"""
kwargs = {'destination':destination}
if type( destination ) == type( " " ):
if not re.search( '^DIRAC.', destination ) and not destination.lower() == 'any':
result = self.__checkSiteIsValid( destination )
if not result['OK']:
return self._reportError( '%s is not a valid destination site' % ( destination ), **kwargs )
description = 'User specified destination site'
self._addParameter( self.workflow, 'Site', 'JDL', destination, description )
elif type( destination ) == list:
for site in destination:
if not re.search( '^DIRAC.', site ) and not site.lower() == 'any':
result = self.__checkSiteIsValid( site )
if not result['OK']:
return self._reportError( '%s is not a valid destination site' % ( destination ), **kwargs )
destSites = ';'.join( destination )
description = 'List of sites selected by user'
self._addParameter( self.workflow, 'Site', 'JDL', destSites, description )
else:
return self._reportError( '%s is not a valid destination site, expected string' % ( destination ), **kwargs )
return S_OK()
#############################################################################
def __checkSiteIsValid( self, site ):
"""Internal function to check that a site name is valid.
"""
sites = getSiteCEMapping()
if not sites['OK']:
return S_ERROR( 'Could not get site CE mapping' )
siteList = sites['Value'].keys()
if not site in siteList:
return S_ERROR( 'Specified site %s is not in list of defined sites' % site )
return S_OK( '%s is valid' % site )
#############################################################################
def setDestinationCE( self, ceName, diracSite = '' ):
""" Developer function.
Allows to direct a job to a particular Grid CE.
"""
kwargs = {'ceName':ceName}
if not diracSite:
diracSite = getSiteForCE( ceName )
if not diracSite['OK']:
return self._reportError( diracSite['Message'], **kwargs )
if not diracSite['Value']:
return self._reportError( 'No DIRAC site name found for CE %s' % ( ceName ), **kwargs )
diracSite = diracSite['Value']
self.setDestination( diracSite )
# Keep GridRequiredCEs for backward compatibility
self._addJDLParameter( 'GridRequiredCEs', ceName )
self._addJDLParameter( 'GridCE', ceName )
return S_OK()
#############################################################################
def setBannedSites( self, sites ):
"""Helper function.
Can specify a desired destination site for job. This can be useful
for debugging purposes but often limits the possible candidate sites
and overall system response time.
Example usage:
>>> job = Job()
>>> job.setBannedSites(['LCG.GRIDKA.de','LCG.CNAF.it'])
:param sites: single site string or list
:type sites: string or list
"""
if type( sites ) == list and len( sites ):
bannedSites = ';'.join( sites )
description = 'List of sites excluded by user'
self._addParameter( self.workflow, 'BannedSites', 'JDL', bannedSites, description )
elif type( sites ) == type( " " ):
description = 'Site excluded by user'
self._addParameter( self.workflow, 'BannedSites', 'JDL', sites, description )
else:
kwargs = {'sites':sites}
return self._reportError( 'Expected site string or list of sites', **kwargs )
return S_OK()
#############################################################################
def setOwner( self, ownerProvided ):
"""Developer function.
Normally users should always specify their immutable DIRAC nickname.
"""
if not type( ownerProvided ) == type( " " ):
return self._reportError( 'Expected string for owner', **{'ownerProvided':ownerProvided} )
self._addParameter( self.workflow, 'Owner', 'JDL', ownerProvided, 'User specified ID' )
return S_OK()
#############################################################################
def setOwnerGroup( self, ownerGroup ):
"""Developer function.
Allows to force expected owner group of proxy.
"""
if not type( ownerGroup ) == type( " " ):
return self._reportError( 'Expected string for job owner group', **{'ownerGroup':ownerGroup} )
self._addParameter( self.workflow, 'OwnerGroup', 'JDL', ownerGroup, 'User specified owner group.' )
return S_OK()
#############################################################################
def setOwnerDN( self, ownerDN ):
"""Developer function.
Allows to force expected owner DN of proxy.
"""
if not type( ownerDN ) == type( " " ):
return self._reportError( 'Expected string for job owner DN', **{'ownerGroup':ownerDN} )
self._addParameter( self.workflow, 'OwnerDN', 'JDL', ownerDN, 'User specified owner DN.' )
return S_OK()
#############################################################################
def setType( self, jobType ):
"""Developer function.
Specify job type for testing purposes.
"""
if not type( jobType ) == type( " " ):
return self._reportError( 'Expected string for job type', **{'jobType':jobType} )
self._addParameter( self.workflow, 'JobType', 'JDL', jobType, 'User specified type' )
self.type = jobType
return S_OK()
#############################################################################
def setTag( self, tags ):
""" Set the Tags job requirements
Example usage:
>>> job = Job()
>>> job.setTag( ['WholeNode','8GBMemory'] )
:param tags: single tag string or a list of tags
:type tags: string or list
"""
if type( tags ) in types.StringTypes:
tagValue = tags
elif type( tags ) == types.ListType:
tagValue = ";".join( tags )
else:
return self._reportError( 'Expected string or list for job tags', tags = tags )
self._addParameter( self.workflow, 'Tags', 'JDL', tagValue, 'User specified job tags' )
self.tags = tags
return S_OK()
#############################################################################
def _setSoftwareTags( self, tags ):
"""Developer function.
Choose any software tags if desired. These are not compulsory but will ensure jobs only
arrive at an LCG site where the software is preinstalled. Without the tags, missing software is
installed automatically by the Job Agent.
Example usage:
>>> job=Job()
>>> job.setSoftwareTags(['VO-lhcb-Brunel-v30r17','VO-lhcb-Boole-v12r10','VO-lhcb-Gauss-v25r12'])
:param tags: software tags
:type tags: string or list
"""
if type( tags ) == type( " " ):
self._addParameter( self.workflow, 'SoftwareTag', 'JDL', tags, 'VO software tag' )
elif type( tags ) == list:
swTags = ';'.join( tags )
self._addParameter( self.workflow, 'SoftwareTag', 'JDL', swTags, 'List of VO software tags' )
else:
kwargs = {'tags':tags}
return self._reportError( 'Expected String or List of software tags', **kwargs )
return S_OK()
#############################################################################
def setJobGroup( self, jobGroup ):
"""Helper function.
Allows to group certain jobs according to an ID.
Example usage:
>>> job = Job()
>>> job.setJobGroup('Bs2JPsiPhi')
:param jobGroup: JobGroup name
:type jobGroup: string
"""
if not type( jobGroup ) == type( " " ):
return self._reportError( 'Expected string for job group name', **{'jobGroup':jobGroup} )
description = 'User specified job group'
self._addParameter( self.workflow, 'JobGroup', 'JDL', jobGroup, description )
return S_OK()
#############################################################################
def setLogLevel( self, logLevel ):
"""Helper function.
Optionally specify a DIRAC logging level for the job, e.g.
ALWAYS, INFO, VERBOSE, WARN, DEBUG
by default this is set to the info level.
Example usage:
>>> job = Job()
>>> job.setLogLevel('debug')
:param logLevel: Logging level
:type logLevel: string
"""
kwargs = {'logLevel':logLevel}
if type( logLevel ) in types.StringTypes:
if logLevel.upper() in gLogger._logLevels.getLevels():
description = 'User specified logging level'
self.logLevel = logLevel
self._addParameter( self.workflow, 'LogLevel', 'JDL', logLevel, description )
else:
return self._reportError( 'Error Level "%s" not valid' % logLevel, **kwargs )
else:
return self._reportError( 'Expected string for logging level', **kwargs )
return S_OK()
#############################################################################
def setConfigArgs( self, cfgString ):
"""Developer function. Allow to pass arbitrary settings to the payload
configuration service environment.
"""
if not type( cfgString ) == type( " " ):
return self._reportError( 'Expected string for DIRAC Job Config Args', **{'cfgString':cfgString} )
description = 'User specified cfg settings'
self._addParameter( self.workflow, 'JobConfigArgs', 'JDL', cfgString, description )
return S_OK()
#############################################################################
def setExecutionEnv( self, environmentDict ):
"""Helper function.
Optionally specify a dictionary of key, value pairs to be set before
the job executes e.g. {'MYVAR':3}
The standard application environment variables are always set so this
is intended for user variables only.
Example usage:
>>> job = Job()
>>> job.setExecutionEnv({'<MYVARIABLE>':'<VALUE>'})
:param environmentDict: Environment variables
:type environmentDict: dictionary
"""
kwargs = {'environmentDict':environmentDict}
if not type( environmentDict ) == type( {} ):
return self._reportError( 'Expected dictionary of environment variables', **kwargs )
if environmentDict:
environment = []
for var, val in environmentDict.items():
try:
environment.append( '='.join( [str( var ), urllib.quote( str( val ) )] ) )
except Exception:
return self._reportError( 'Expected string for environment variable key value pairs', **kwargs )
envStr = ';'.join( environment )
description = 'Env vars specified by user'
self._addParameter( self.workflow, 'ExecutionEnvironment', 'JDL', envStr, description )
return S_OK()
#############################################################################
def execute( self ):
"""Developer function. Executes the job locally.
"""
self.workflow.createCode()
self.workflow.execute()
#############################################################################
def _getParameters( self ):
"""Developer function.
Method to return the workflow parameters.
"""
wfParams = {}
params = self.workflow.parameters
for par in params:
wfParams[par.getName()] = par.getValue()
return wfParams
#############################################################################
def _dumpParameters( self, showType = None ):
"""Developer function.
Method to print the workflow parameters.
"""
paramsDict = {}
paramList = self.workflow.parameters
for param in paramList:
paramsDict[param.getName()] = {'type':param.getType(), 'value':param.getValue()}
self.log.info( '--------------------------------------' )
self.log.info( 'Workflow parameter summary: ' )
self.log.info( '--------------------------------------' )
#print self.workflow.parameters
#print params.getParametersNames()
for name, _props in paramsDict.items():
ptype = paramsDict[name]['type']
value = paramsDict[name]['value']
if showType:
if ptype == showType:
self.log.info( 'NAME: %s\nTYPE: %s\nVALUE: %s ' % ( name, ptype, value ) )
self.log.info( '--------------------------------------' )
else:
self.log.info( 'NAME: %s\nTYPE: %s\nVALUE: %s ' % ( name, ptype, value ) )
self.log.info( '--------------------------------------' )
#############################################################################
def __setJobDefaults( self ):
"""Set job default values. Note that the system configuration is set to "ANY".
"""
self._addParameter( self.workflow, 'JobType', 'JDL', self.type, 'Job Type' )
self._addParameter( self.workflow, 'Priority', 'JDL', self.priority, 'User Job Priority' )
self._addParameter( self.workflow, 'JobGroup', 'JDL', self.group, 'Name of the JobGroup' )
self._addParameter( self.workflow, 'JobName', 'JDL', self.name, 'Name of Job' )
#self._addParameter(self.workflow,'DIRACSetup','JDL',self.setup,'DIRAC Setup')
self._addParameter( self.workflow, 'Site', 'JDL', self.site, 'Site Requirement' )
self._addParameter( self.workflow, 'Origin', 'JDL', self.origin, 'Origin of client' )
self._addParameter( self.workflow, 'StdOutput', 'JDL', self.stdout, 'Standard output file' )
self._addParameter( self.workflow, 'StdError', 'JDL', self.stderr, 'Standard error file' )
self._addParameter( self.workflow, 'InputData', 'JDL', '', 'Default null input data value' )
self._addParameter( self.workflow, 'LogLevel', 'JDL', self.logLevel, 'Job Logging Level' )
#Those 2 below are need for on-site resolution
self._addParameter( self.workflow, 'ParametricInputData', 'string', '',
'Default null parametric input data value' )
self._addParameter( self.workflow, 'ParametricInputSandbox', 'string', '',
'Default null parametric input sandbox value' )
self._addParameter( self.workflow, 'ParametricParameters', 'string', '',
'Default null parametric input parameters value' )
#############################################################################
def _addParameter( self, wObject, name, ptype, value, description, io = 'input' ):
""" Internal Function
Adds a parameter to the object.
"""
if io == 'input':
inBool = True
outBool = False
elif io == 'output':
inBool = False
outBool = True
else:
raise TypeError( 'I/O flag is either input or output' )
par = Parameter( name, value, ptype, "", "", inBool, outBool, description )
wObject.addParameter( Parameter( parameter = par ) )
return par
############################################################################
def _resolveInputSandbox( self, inputSandbox ):
""" Internal function.
Resolves wildcards for input sandbox files. This is currently linux
specific and should be modified.
"""
resolvedIS = []
for i in inputSandbox:
if not re.search( '\*', i ):
if not os.path.isdir( i ):
resolvedIS.append( i )
for name in inputSandbox:
if re.search( '\*', name ): #escape the star character...
cmd = 'ls -d ' + name
output = shellCall( 10, cmd )
if not output['OK']:
self.log.error( 'Could not perform: ', cmd )
elif output['Value'][0]:
self.log.error(" Failed getting the files ", output['Value'][2])
else:
files = output['Value'][1].split()
for check in files:
if os.path.isfile( check ):
self.log.verbose( 'Found file ' + check + ' appending to Input Sandbox' )
resolvedIS.append( check )
if os.path.isdir( check ):
if re.search( '/$', check ): #users can specify e.g. /my/dir/lib/
check = check[:-1]
tarname = os.path.basename( check )
directory = os.path.dirname( check ) #if just the directory this is null
if directory:
cmd = 'tar cfz ' + tarname + '.tar.gz ' + ' -C ' + directory + ' ' + tarname
else:
cmd = 'tar cfz ' + tarname + '.tar.gz ' + tarname
output = shellCall( 60, cmd )
if not output['OK']:
self.log.error( 'Could not perform: %s' % ( cmd ) )
resolvedIS.append( tarname + '.tar.gz' )
self.log.verbose( 'Found directory ' + check + ', appending ' + check + '.tar.gz to Input Sandbox' )
if os.path.isdir( name ):
self.log.verbose( 'Found specified directory ' + name + ', appending ' + name + '.tar.gz to Input Sandbox' )
if re.search( '/$', name ): #users can specify e.g. /my/dir/lib/
name = name[:-1]
tarname = os.path.basename( name )
directory = os.path.dirname( name ) #if just the directory this is null
if directory:
cmd = 'tar cfz ' + tarname + '.tar.gz ' + ' -C ' + directory + ' ' + tarname
else:
cmd = 'tar cfz ' + tarname + '.tar.gz ' + tarname
output = shellCall( 60, cmd )
if not output['OK']:
self.log.error( 'Could not perform: %s' % ( cmd ) )
else:
resolvedIS.append( tarname + '.tar.gz' )
return resolvedIS
#############################################################################
def _toXML( self ):
"""Creates an XML representation of itself as a Job.
"""
return self.workflow.toXML()
#############################################################################
def _toJDL( self, xmlFile = '' ): #messy but need to account for xml file being in /tmp/guid dir
"""Creates a JDL representation of itself as a Job.
"""
#Check if we have to do old bootstrap...
classadJob = ClassAd( '[]' )
paramsDict = {}
params = self.workflow.parameters # ParameterCollection object
paramList = params
for param in paramList:
paramsDict[param.getName()] = {'type':param.getType(), 'value':param.getValue()}
scriptname = 'jobDescription.xml'
arguments = []
if self.script:
if os.path.exists( self.script ):
scriptname = os.path.abspath( self.script )
self.log.verbose( 'Found script name %s' % scriptname )
else:
if xmlFile:
self.log.verbose( 'Found XML File %s' % xmlFile )
scriptname = xmlFile
arguments.append( os.path.basename( scriptname ) )
self.addToInputSandbox.append( scriptname )
if paramsDict.has_key( 'LogLevel' ):
if paramsDict['LogLevel']['value']:
arguments.append( '-o LogLevel=%s' % ( paramsDict['LogLevel']['value'] ) )
else:
self.log.warn( 'Job LogLevel defined with null value' )
if paramsDict.has_key( 'DIRACSetup' ):
if paramsDict['DIRACSetup']['value']:
arguments.append( '-o DIRAC/Setup=%s' % ( paramsDict['DIRACSetup']['value'] ) )
else:
self.log.warn( 'Job DIRACSetup defined with null value' )
if paramsDict.has_key( 'JobMode' ):
if paramsDict['JobMode']['value']:
arguments.append( '-o JobMode=%s' % ( paramsDict['JobMode']['value'] ) )
else:
self.log.warn( 'Job Mode defined with null value' )
if paramsDict.has_key( 'JobConfigArgs' ):
if paramsDict['JobConfigArgs']['value']:
arguments.append( '%s' % ( paramsDict['JobConfigArgs']['value'] ) )
else:
self.log.warn( 'JobConfigArgs defined with null value' )
classadJob.insertAttributeString( 'Executable', self.executable )
self.addToOutputSandbox.append( self.stderr )
self.addToOutputSandbox.append( self.stdout )
#Extract i/o sandbox parameters from steps and any input data parameters
#to do when introducing step-level api...
#To add any additional files to input and output sandboxes
if self.addToInputSandbox:
extraFiles = ';'.join( self.addToInputSandbox )
if paramsDict.has_key( 'InputSandbox' ):
currentFiles = paramsDict['InputSandbox']['value']
finalInputSandbox = currentFiles + ';' + extraFiles
uniqueInputSandbox = uniqueElements( finalInputSandbox.split( ';' ) )
paramsDict['InputSandbox']['value'] = ';'.join( uniqueInputSandbox )
self.log.verbose( 'Final unique Input Sandbox %s' % ( ';'.join( uniqueInputSandbox ) ) )
else:
paramsDict['InputSandbox'] = {}
paramsDict['InputSandbox']['value'] = extraFiles
paramsDict['InputSandbox']['type'] = 'JDL'
if self.addToOutputSandbox:
extraFiles = ';'.join( self.addToOutputSandbox )
if paramsDict.has_key( 'OutputSandbox' ):
currentFiles = paramsDict['OutputSandbox']['value']
finalOutputSandbox = currentFiles + ';' + extraFiles
uniqueOutputSandbox = uniqueElements( finalOutputSandbox.split( ';' ) )
paramsDict['OutputSandbox']['value'] = ';'.join( uniqueOutputSandbox )
self.log.verbose( 'Final unique Output Sandbox %s' % ( ';'.join( uniqueOutputSandbox ) ) )
else:
paramsDict['OutputSandbox'] = {}
paramsDict['OutputSandbox']['value'] = extraFiles
paramsDict['OutputSandbox']['type'] = 'JDL'
if self.addToInputData:
extraFiles = ';'.join( self.addToInputData )
if paramsDict.has_key( 'InputData' ):
currentFiles = paramsDict['InputData']['value']
finalInputData = extraFiles
if currentFiles:
finalInputData = currentFiles + ';' + extraFiles
uniqueInputData = uniqueElements( finalInputData.split( ';' ) )
paramsDict['InputData']['value'] = ';'.join( uniqueInputData )
self.log.verbose( 'Final unique Input Data %s' % ( ';'.join( uniqueInputData ) ) )
else:
paramsDict['InputData'] = {}
paramsDict['InputData']['value'] = extraFiles
paramsDict['InputData']['type'] = 'JDL'
# Handle here the Parametric values
if self.parametric:
for pType in ['InputData', 'InputSandbox']:
if self.parametric.has_key( pType ):
if paramsDict.has_key( pType ) and paramsDict[pType]['value']:
pData = self.parametric[pType]
# List of lists case
currentFiles = paramsDict[pType]['value'].split( ';' )
tmpList = []
if type( pData[0] ) == list:
for pElement in pData:
tmpList.append( currentFiles + pElement )
else:
for pElement in pData:
tmpList.append( currentFiles + [pElement] )
self.parametric[pType] = tmpList
paramsDict[pType] = {}
paramsDict[pType]['value'] = "%s"
paramsDict[pType]['type'] = 'JDL'
self.parametric['files'] = self.parametric[pType]
arguments.append( ' -p Parametric' + pType + '=%s' )
break
if self.parametric.has_key( 'files' ):
paramsDict['Parameters'] = {}
paramsDict['Parameters']['value'] = self.parametric['files']
paramsDict['Parameters']['type'] = 'JDL'
if self.parametric.has_key( 'GenericParameters' ):
paramsDict['Parameters'] = {}
paramsDict['Parameters']['value'] = self.parametric['GenericParameters']
paramsDict['Parameters']['type'] = 'JDL'
arguments.append( ' -p ParametricParameters=%s' )
##This needs to be put here so that the InputData and/or InputSandbox parameters for parametric jobs are processed
classadJob.insertAttributeString( 'Arguments', ' '.join( arguments ) )
#Add any JDL parameters to classad obeying lists with ';' rule
for name, props in paramsDict.items():
ptype = props['type']
value = props['value']
if name.lower() == 'requirements' and ptype == 'JDL':
self.log.verbose( 'Found existing requirements: %s' % ( value ) )
if re.search( '^JDL', ptype ):
if type( value ) == list:
if type( value[0] ) == list:
classadJob.insertAttributeVectorStringList( name, value )
else:
classadJob.insertAttributeVectorString( name, value )
elif value == "%s":
classadJob.insertAttributeInt( name, value )
elif not re.search( ';', value ) or name == 'GridRequirements': #not a nice fix...
classadJob.insertAttributeString( name, value )
else:
classadJob.insertAttributeVectorString( name, value.split( ';' ) )
self.addToInputSandbox.remove( scriptname )
self.addToOutputSandbox.remove( self.stdout )
self.addToOutputSandbox.remove( self.stderr )
jdl = classadJob.asJDL()
start = jdl.find( '[' )
end = jdl.rfind( ']' )
return jdl[( start + 1 ):( end - 1 )]
#############################################################################
def _setParamValue( self, name, value ):
"""Internal Function. Sets a parameter value, used for production.
"""
return self.workflow.setValue( name, value )
#############################################################################
def _addJDLParameter( self, name, value ):
"""Developer function, add an arbitrary JDL parameter.
"""
self._addParameter( self.workflow, name, 'JDL', value, 'Optional JDL parameter added' )
return self.workflow.setValue( name, value )
#############################################################################
def runLocal( self, dirac = None ):
""" The dirac (API) object is for local submission.
"""
if dirac is None:
dirac = Dirac()
return dirac.submit( self, mode = 'local' )
#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#
|
marcelovilaca/DIRAC
|
Interfaces/API/Job.py
|
Python
|
gpl-3.0
| 47,518
|
[
"DIRAC"
] |
10cf6c9f457d466929460586a9ca9ad8a30a31e0e3a7ecf656ae1730ce9f11d2
|
# Orca
#
# Copyright 2008-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the
# Free Software Foundation, Inc., Franklin Street, Fifth Floor,
# Boston MA 02110-1301 USA.
__id__ = "$Id$"
__version__ = "$Revision$"
__date__ = "$Date$"
__copyright__ = "Copyright (c) 2008-2009 Sun Microsystems Inc."
__license__ = "LGPL"
import orca.tutorialgenerator as tutorialgenerator
from orca.orca_i18n import _ # for gettext support
class TutorialGenerator(tutorialgenerator.TutorialGenerator):
"""Overridden here so that we can provide a custom message regarding
how to move focus to the search results after a search has been
executed. This is needed because focus remains in the Search entry,
and an object in between the entry and the list of results clears
the search automatically when given focus."""
def __init__(self, script):
tutorialgenerator.TutorialGenerator.__init__(self, script)
def _getTutorialForText(self, obj, alreadyFocused, forceTutorial):
"""Get the tutorial string for a text object.
Arguments:
- obj: the text component
- alreadyFocused: False if object just received focus
- forceTutorial: used for when whereAmI really needs the tutorial
string
Returns a list of tutorial utterances to be spoken for the object.
"""
utterances = tutorialgenerator.TutorialGenerator.\
_getTutorialForText(self, obj, alreadyFocused, forceTutorial)
if utterances and self._script.isSearchEntry(obj):
# Translators: This is the tutorial string associated with a
# specific search field in the Packagemanager application.
# It is designed to inform the user how to move directly to
# the search results after the search has been completed.
#
utterances.append(_("Use Ctrl+L to move focus to the results."))
self._debugGenerator("_getTutorialForText",
obj,
alreadyFocused,
utterances)
return utterances
|
Alberto-Beralix/Beralix
|
i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/packagemanager/tutorialgenerator.py
|
Python
|
gpl-3.0
| 2,744
|
[
"ORCA"
] |
0fff3e280188d3d4bc7a9e5eea8182036b1fb6ec5171abcf3e6be5bf778b538b
|
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# @END LICENSE
#
"""
This module contains a few small sphinx extensions.
They are mainly used to help with the generation
of BPS's own documentation, but some other projects
use them as well, so they are kept here.
"""
import re
import os.path
__version__ = "1.4"
def get_theme_dir():
"return path to directory containing sphinx themes in this package"
return os.path.abspath(os.path.join(__file__,os.path.pardir, "themes"))
def get_version(release):
"derive short version string from longer release"
return re.match("(\d+\.\d+)", release).group(1)
|
andysim/psi4
|
doc/sphinxman/source/psi4doc/__init__.py
|
Python
|
gpl-2.0
| 1,500
|
[
"Psi4"
] |
d86fec54ab6d7fa09ec1f840a207620850e2f97d81cbcb58cc16cc7a2b88f633
|
"""
Copyright (c) 2016 Jet Propulsion Laboratory,
California Institute of Technology. All rights reserved
"""
import logging
from calendar import timegm, monthrange
from datetime import datetime
import numpy as np
from nexustiles.nexustiles import NexusTileService
from webservice.NexusHandler import nexus_handler, SparkHandler, DEFAULT_PARAMETERS_SPEC
from webservice.webmodel import NexusResults, NexusProcessingException, NoDataException
@nexus_handler
class ClimMapSparkHandlerImpl(SparkHandler):
name = "Climatology Map Spark"
path = "/climMapSpark"
description = "Computes a Latitude/Longitude Time Average map for a given month given an arbitrary geographical area and year range"
params = DEFAULT_PARAMETERS_SPEC
singleton = True
def __init__(self):
SparkHandler.__init__(self)
self.log = logging.getLogger(__name__)
# self.log.setLevel(logging.DEBUG)
@staticmethod
def _map(tile_in_spark):
tile_bounds = tile_in_spark[0]
(min_lat, max_lat, min_lon, max_lon,
min_y, max_y, min_x, max_x) = tile_bounds
startTime = tile_in_spark[1]
endTime = tile_in_spark[2]
ds = tile_in_spark[3]
tile_service = NexusTileService()
# print 'Started tile', tile_bounds
# sys.stdout.flush()
tile_inbounds_shape = (max_y - min_y + 1, max_x - min_x + 1)
days_at_a_time = 90
# days_at_a_time = 30
# days_at_a_time = 7
# days_at_a_time = 1
# print 'days_at_a_time = ', days_at_a_time
t_incr = 86400 * days_at_a_time
sum_tile = np.array(np.zeros(tile_inbounds_shape, dtype=np.float64))
cnt_tile = np.array(np.zeros(tile_inbounds_shape, dtype=np.uint32))
t_start = startTime
while t_start <= endTime:
t_end = min(t_start + t_incr, endTime)
# t1 = time()
# print 'nexus call start at time %f' % t1
# sys.stdout.flush()
nexus_tiles = \
ClimMapSparkHandlerImpl.query_by_parts(tile_service,
min_lat, max_lat,
min_lon, max_lon,
ds,
t_start,
t_end,
part_dim=2)
# nexus_tiles = \
# tile_service.get_tiles_bounded_by_box(min_lat, max_lat,
# min_lon, max_lon,
# ds=ds,
# start_time=t_start,
# end_time=t_end)
# t2 = time()
# print 'nexus call end at time %f' % t2
# print 'secs in nexus call: ', t2-t1
# sys.stdout.flush()
# print 't %d to %d - Got %d tiles' % (t_start, t_end,
# len(nexus_tiles))
# for nt in nexus_tiles:
# print nt.granule
# print nt.section_spec
# print 'lat min/max:', np.ma.min(nt.latitudes), np.ma.max(nt.latitudes)
# print 'lon min/max:', np.ma.min(nt.longitudes), np.ma.max(nt.longitudes)
# sys.stdout.flush()
for tile in nexus_tiles:
tile.data.data[:, :] = np.nan_to_num(tile.data.data)
sum_tile += tile.data.data[0, min_y:max_y + 1, min_x:max_x + 1]
cnt_tile += (~tile.data.mask[0,
min_y:max_y + 1,
min_x:max_x + 1]).astype(np.uint8)
t_start = t_end + 1
# print 'cnt_tile = ', cnt_tile
# cnt_tile.mask = ~(cnt_tile.data.astype(bool))
# sum_tile.mask = cnt_tile.mask
# avg_tile = sum_tile / cnt_tile
# stats_tile = [[{'avg': avg_tile.data[y,x], 'cnt': cnt_tile.data[y,x]} for x in range(tile_inbounds_shape[1])] for y in range(tile_inbounds_shape[0])]
# print 'Finished tile', tile_bounds
# print 'Tile avg = ', avg_tile
# sys.stdout.flush()
return ((min_lat, max_lat, min_lon, max_lon), (sum_tile, cnt_tile))
def _month_from_timestamp(self, t):
return datetime.utcfromtimestamp(t).month
def calc(self, computeOptions, **args):
"""
:param computeOptions: StatsComputeOptions
:param args: dict
:return:
"""
spark_master, spark_nexecs, spark_nparts = computeOptions.get_spark_cfg()
self._setQueryParams(computeOptions.get_dataset()[0],
(float(computeOptions.get_min_lat()),
float(computeOptions.get_max_lat()),
float(computeOptions.get_min_lon()),
float(computeOptions.get_max_lon())),
start_year=computeOptions.get_start_year(),
end_year=computeOptions.get_end_year(),
clim_month=computeOptions.get_clim_month(),
spark_master=spark_master,
spark_nexecs=spark_nexecs,
spark_nparts=spark_nparts)
self._startTime = timegm((self._startYear, 1, 1, 0, 0, 0))
self._endTime = timegm((self._endYear, 12, 31, 23, 59, 59))
if 'CLIM' in self._ds:
raise NexusProcessingException(reason="Cannot compute Latitude/Longitude Time Average map on a climatology",
code=400)
nexus_tiles = self._find_global_tile_set()
# print 'tiles:'
# for tile in nexus_tiles:
# print tile.granule
# print tile.section_spec
# print 'lat:', tile.latitudes
# print 'lon:', tile.longitudes
# nexus_tiles)
if len(nexus_tiles) == 0:
raise NoDataException(reason="No data found for selected timeframe")
self.log.debug('Found {0} tiles'.format(len(nexus_tiles)))
# for tile in nexus_tiles:
# print 'lats: ', tile.latitudes.compressed()
# print 'lons: ', tile.longitudes.compressed()
self.log.debug('Using Native resolution: lat_res={0}, lon_res={1}'.format(self._latRes, self._lonRes))
nlats = int((self._maxLat - self._minLatCent) / self._latRes) + 1
nlons = int((self._maxLon - self._minLonCent) / self._lonRes) + 1
self.log.debug('nlats={0}, nlons={1}'.format(nlats, nlons))
self.log.debug('center lat range = {0} to {1}'.format(self._minLatCent,
self._maxLatCent))
self.log.debug('center lon range = {0} to {1}'.format(self._minLonCent,
self._maxLonCent))
# Create array of tuples to pass to Spark map function
nexus_tiles_spark = [[self._find_tile_bounds(t),
self._startTime, self._endTime,
self._ds] for t in nexus_tiles]
# print 'nexus_tiles_spark = ', nexus_tiles_spark
# Remove empty tiles (should have bounds set to None)
bad_tile_inds = np.where([t[0] is None for t in nexus_tiles_spark])[0]
for i in np.flipud(bad_tile_inds):
del nexus_tiles_spark[i]
num_nexus_tiles_spark = len(nexus_tiles_spark)
self.log.debug('Created {0} spark tiles'.format(num_nexus_tiles_spark))
# Expand Spark map tuple array by duplicating each entry N times,
# where N is the number of ways we want the time dimension carved up.
# (one partition per year in this case).
num_years = self._endYear - self._startYear + 1
nexus_tiles_spark = np.repeat(nexus_tiles_spark, num_years, axis=0)
self.log.debug('repeated len(nexus_tiles_spark) = {0}'.format(len(nexus_tiles_spark)))
# Set the time boundaries for each of the Spark map tuples.
# Every Nth element in the array gets the same time bounds.
spark_part_time_ranges = \
np.repeat(np.array([[timegm((y, self._climMonth, 1, 0, 0, 0)),
timegm((y, self._climMonth,
monthrange(y, self._climMonth)[1],
23, 59, 59))]
for y in range(self._startYear,
self._endYear + 1)]),
num_nexus_tiles_spark,
axis=0).reshape((len(nexus_tiles_spark), 2))
self.log.debug('spark_part_time_ranges={0}'.format(spark_part_time_ranges))
nexus_tiles_spark[:, 1:3] = spark_part_time_ranges
# print 'nexus_tiles_spark final = '
# for i in range(len(nexus_tiles_spark)):
# print nexus_tiles_spark[i]
# Launch Spark computations
rdd = self._sc.parallelize(nexus_tiles_spark, self._spark_nparts)
sum_count_part = rdd.map(self._map)
sum_count = \
sum_count_part.combineByKey(lambda val: val,
lambda x, val: (x[0] + val[0],
x[1] + val[1]),
lambda x, y: (x[0] + y[0], x[1] + y[1]))
avg_tiles = \
sum_count.map(lambda (bounds, (sum_tile, cnt_tile)):
(bounds, [[{'avg': (sum_tile[y, x] / cnt_tile[y, x])
if (cnt_tile[y, x] > 0) else 0.,
'cnt': cnt_tile[y, x]}
for x in
range(sum_tile.shape[1])]
for y in
range(sum_tile.shape[0])])).collect()
# Combine subset results to produce global map.
#
# The tiles below are NOT Nexus objects. They are tuples
# with the time avg map data and lat-lon bounding box.
a = np.zeros((nlats, nlons), dtype=np.float64, order='C')
n = np.zeros((nlats, nlons), dtype=np.uint32, order='C')
for tile in avg_tiles:
if tile is not None:
((tile_min_lat, tile_max_lat, tile_min_lon, tile_max_lon),
tile_stats) = tile
tile_data = np.ma.array(
[[tile_stats[y][x]['avg'] for x in range(len(tile_stats[0]))] for y in range(len(tile_stats))])
tile_cnt = np.array(
[[tile_stats[y][x]['cnt'] for x in range(len(tile_stats[0]))] for y in range(len(tile_stats))])
tile_data.mask = ~(tile_cnt.astype(bool))
y0 = self._lat2ind(tile_min_lat)
y1 = y0 + tile_data.shape[0] - 1
x0 = self._lon2ind(tile_min_lon)
x1 = x0 + tile_data.shape[1] - 1
if np.any(np.logical_not(tile_data.mask)):
self.log.debug(
'writing tile lat {0}-{1}, lon {2}-{3}, map y {4}-{5}, map x {6}-{7}'.format(tile_min_lat,
tile_max_lat,
tile_min_lon,
tile_max_lon, y0,
y1, x0, x1))
a[y0:y1 + 1, x0:x1 + 1] = tile_data
n[y0:y1 + 1, x0:x1 + 1] = tile_cnt
else:
self.log.debug(
'All pixels masked in tile lat {0}-{1}, lon {2}-{3}, map y {4}-{5}, map x {6}-{7}'.format(
tile_min_lat, tile_max_lat,
tile_min_lon, tile_max_lon,
y0, y1, x0, x1))
# Store global map in a NetCDF file.
self._create_nc_file(a, 'clmap.nc', 'val')
# Create dict for JSON response
results = [[{'avg': a[y, x], 'cnt': int(n[y, x]),
'lat': self._ind2lat(y), 'lon': self._ind2lon(x)}
for x in range(a.shape[1])] for y in range(a.shape[0])]
return ClimMapSparkResults(results=results, meta={}, computeOptions=computeOptions)
class ClimMapSparkResults(NexusResults):
def __init__(self, results=None, meta=None, computeOptions=None):
NexusResults.__init__(self, results=results, meta=meta, stats=None, computeOptions=computeOptions)
|
dataplumber/nexus
|
analysis/webservice/algorithms_spark/ClimMapSpark.py
|
Python
|
apache-2.0
| 12,964
|
[
"NetCDF"
] |
dd2669fedd86100faa89dde1f11d61c6ebed7a18cf90bec882477aa53598fd58
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# kernel_test - tests some kernel functions in standalone mode
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# MiG is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# -- END_HEADER ---
#
"""
Created by Jan Wiberg on 2010-03-29.
Copyright (c) 2010 __MyCompanyName__. All rights reserved.
"""
import sys, time, os
from core.entities import *
from core.configuration import *
import core.kernel as kernel
def main():
opt = Configuration()
node_id = 8000
opt.backingstore = '/tmp/node%s' % node_id
opt.backingstorestate = '../tests/nettest_node%s.bsc' % node_id
opt.serverport = node_id
opt.maxcopies = 0
opt.mincopies = 0
opt.logquiet = False
opt.logverbose = True
opt.logverbosity = 3
opt.validate()
k = kernel.Kernel(opt)
k.fsinit()
test_filename = 'hello'
test_path = os.path.join(os.sep, test_filename)
print "Instance started"
try:
print "!! Getattr on '/': %s" % k.getattr("/", None)
print "!! Readdir on '/': %s" % k.readdir("/", 0, None)
# Root dir may be empty
if test_filename in k.readdir("/", 0, None):
f = GRSFile(test_path, os.O_RDONLY)
assert f.file is not None and f.file >= 1
print "!! Read %s:\n%s" % (test_path, f.read(-1, 0))
print "!! Success on last test"
attrs = f.fgetattr()
print "!! Fgetattrs %s" % attrs
import random
filename = '/file%d' % random.randint(1000, 9999)
print "!! Writing to %s" % filename
w_f = GRSFile(filename, os.O_CREAT|os.O_WRONLY)
# print "Errno EROFS %d" % errno.EROFS
assert w_f.file is not None and w_f.file >= 1
w_f.write("Some string goes here %s\n" % random.randint(0, 10000000), 0)
w_f.flush()
w_f.release(w_f.open_args[1])
r_f = GRSFile(filename, os.O_RDONLY)
assert r_f.file is not None and r_f.file >= 1
print "!! Read: ", r_f.read(-1, 0)
r_f.release(r_f.open_args[1])
# append mode
filename = "/file_a"
print "!! appending to %s" % filename
w_f = GRSFile(filename, os.O_CREAT|os.O_WRONLY|os.O_APPEND)
assert w_f.file is not None and w_f.file >= 1
w_f.write("mary", 0)
w_f.flush()
w_f.release(w_f.open_args[1])
print "!! -- first part written"
w_f = GRSFile(filename, os.O_WRONLY|os.O_APPEND)
assert w_f.file is not None and w_f.file >= 1
w_f.write("mary", 5)
w_f.flush()
w_f.release(w_f.open_args[1])
r_f = GRSFile(filename, os.O_RDONLY)
assert r_f.file is not None and r_f.file >= 1
print "!! Read: ", r_f.read(-1, 0)
r_f.release(r_f.open_args[1])
# Root dir may be empty
if test_filename in k.readdir("/", 0, None):
k.utime(test_path, (time.time(), time.time()), None)
else:
print "!! Creating test file %s for future runs" % test_path
w_f = GRSFile(test_path, os.O_CREAT|os.O_WRONLY)
assert w_f.file is not None and w_f.file >= 1
w_f.write("Hello grid file system!\n", 0)
w_f.flush()
w_f.release(w_f.open_args[1])
finally:
k.fshalt()
if __name__ == '__main__':
main()
|
heromod/migrid
|
mig/grsfs-fuse/fs/kernel_test.py
|
Python
|
gpl-2.0
| 4,109
|
[
"Brian"
] |
3605819ee730a789e3b6dfcfdee26e1c0fdac3b8d43922589e69ff6c9fd9580a
|
## Copyright 2016 Kurt Cutajar, Edwin V. Bonilla, Pietro Michiardi, Maurizio Filippone
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
import numpy as np
import tensorflow as tf
## Log-density of a univariate Gaussian distribution
def log_norm_pdf(x, m=0.0, log_v=0.0):
return - 0.5 * tf.log(2 * np.pi) - 0.5 * log_v - 0.5 * tf.square(x - m) / tf.exp(log_v)
## Kullback-Leibler divergence between multivariate Gaussian distributions q and p with diagonal covariance matrices
def DKL_gaussian(mq, log_vq, mp, log_vp):
"""
KL[q || p]
:param mq: vector of means for q
:param log_vq: vector of log-variances for q
:param mp: vector of means for p
:param log_vp: vector of log-variances for p
:return: KL divergence between q and p
"""
log_vp = tf.reshape(log_vp, (-1, 1))
return 0.5 * tf.reduce_sum(log_vp - log_vq + (tf.pow(mq - mp, 2) / tf.exp(log_vp)) + tf.exp(log_vq - log_vp) - 1)
## Draw a tensor of standard normals
def get_normal_samples(ns, din, dout):
""""
:param ns: Number of samples
:param din:
:param dout:
:return:
"""
dx = np.amax(din)
dy = np.amax(dout)
return tf.random_normal(shape=[ns, dx, dy], dtype="float32")
## Log-sum operation
def logsumexp(vals, dim=None):
m = tf.reduce_max(vals, dim)
if dim is None:
return m + tf.log(tf.reduce_sum(tf.exp(vals - m), dim))
else:
return m + tf.log(tf.reduce_sum(tf.exp(vals - tf.expand_dims(m, dim)), dim))
## Get flags from the command line
def get_flags():
flags = tf.app.flags
FLAGS = flags.FLAGS
flags.DEFINE_integer('batch_size', 50, 'Batch size. ')
flags.DEFINE_float('learning_rate', 0.1, 'Initial learning rate.')
flags.DEFINE_integer('n_iterations', 2000, 'Number of iterations (batches) to feed to the DGP')
flags.DEFINE_integer('display_step', 100, 'Display progress every FLAGS.display_step iterations')
flags.DEFINE_integer('mc_train', 30, 'Number of Monte Carlo samples used to compute stochastic gradients')
flags.DEFINE_integer('mc_test', 30, 'Number of Monte Carlo samples for predictions')
flags.DEFINE_integer('n_rff', 10, 'Number of random features for each layer')
flags.DEFINE_integer('df', 1, 'Number of GPs per hidden layer')
flags.DEFINE_integer('nl', 1, 'Number of layers')
flags.DEFINE_string('optimizer', "adagrad", 'Optimizer')
flags.DEFINE_string('kernel_type', "RBF", 'arccosine')
flags.DEFINE_integer('kernel_arccosine_degree', 1, 'Degree parameter of arc-cosine kernel')
flags.DEFINE_boolean('is_ard', False, 'Using ARD kernel or isotropic')
flags.DEFINE_boolean('local_reparam', False, 'Using the local reparameterization trick')
flags.DEFINE_boolean('feed_forward', False, 'Feed original inputs to each layer')
flags.DEFINE_integer('q_Omega_fixed', 0, 'Number of iterations to keep posterior over Omega fixed')
flags.DEFINE_integer('theta_fixed', 0, 'Number of iterations to keep theta fixed')
flags.DEFINE_string('learn_Omega', 'prior_fixed', 'How to treat Omega - fixed (from the prior), optimized, or learned variationally')
flags.DEFINE_integer('duration', 10000000, 'Duration of job in minutes')
# Flags for use in cluster experiments
tf.app.flags.DEFINE_string("dataset", "", "Dataset name")
tf.app.flags.DEFINE_string("fold", "1", "Dataset fold")
tf.app.flags.DEFINE_integer("seed", 0, "Seed for random tf and np operations")
tf.app.flags.DEFINE_boolean("less_prints", False, "Disables evaluations involving the complete dataset without batching")
# Flags to setup distributed exectuion
# Flags for defining the tf.train.ClusterSpec
# These can be set by using the following CLI arguments:
# --ps_hosts=ps0.example.com:2222,ps1.example.com:2222 \
# --worker_hosts=worker0.example.com:2222,worker1.example.com:2222 \
tf.app.flags.DEFINE_string("ps_hosts", "", "Comma-separated list of hostname:port pairs")
tf.app.flags.DEFINE_string("worker_hosts", "", "Comma-separated list of hostname:port pairs")
# Flags for defining the tf.train.Server
tf.app.flags.DEFINE_string("job_name", "", "One of 'ps', 'worker'")
tf.app.flags.DEFINE_integer("task_index", 0, "Index of task within the job")
return FLAGS
## Define the right optimizer for a given flag from command line
def get_optimizer(opt_name, learning_rate):
switcher = {
"adagrad": tf.train.AdagradOptimizer(learning_rate),
"sgd": tf.train.GradientDescentOptimizer(learning_rate),
"adam": tf.train.AdamOptimizer(learning_rate),
"adadelta": tf.train.AdadeltaOptimizer(learning_rate)
}
return switcher.get(opt_name)
|
mauriziofilippone/deep_gp_random_features
|
code/utils.py
|
Python
|
apache-2.0
| 5,184
|
[
"Gaussian"
] |
07ab729a1c1b429ff8920f324878cc4af1794ea4bb833d52fc9d895eaeaec21d
|
import sys, os, inspect
import os, sys, inspect, inviwopy
path_to_current_folder = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
sys.path.append(path_to_current_folder + "/../")
import envisionpy
import envisionpy.hdf5parser
from envisionpy.network import VisualisationManager
# Path to the vasp output directory you wish to visualise
VASP_DIR = path_to_current_folder + "/../unit_testing/resources/partial_charges"
HDF5_FILE = path_to_current_folder + "/../parchg.hdf5"
# Parse for charge density visualisation.
envisionpy.hdf5parser.parchg(HDF5_FILE, VASP_DIR)
# Clear any old network
inviwopy.app.network.clear()
# Initialize inviwo network
visManager = VisualisationManager(HDF5_FILE, inviwopy.app)
visManager.start("parchg", [1, 4], ["total", "total"])
# visManager.subnetworks["parchg"].toggle_iso(True)
|
rartino/ENVISIoN
|
demo/parchg.py
|
Python
|
bsd-2-clause
| 844
|
[
"VASP"
] |
6c6aa1fb6063eb77ea713a7e58cb16971a07fd1d7b2347eaf747e612a205f6c4
|
# -*- coding: utf-8 -*-
"""
This file contains settings required to make ICs for the dust settling test
of Price & Laibe (2015) (see section 4.4 Dust settling in a protoplanetary disc)
This uses a stretched cubic grid with a gaussian vertical density profile as
a starting point (similar to Price & Laibe's hexagonal grid). This method
for generating ICs the same as in PL15.
This file is parsed by testdust.utils.parsePySettings() by running execfile()
on it. Imports can be included in this file, but all modules will be ignored.
Also, before running the generated dust ICs, you may want to adjust dDelta
THIS IS A 2D TEST. It requires ChaNGa be compiled with NDSPH=2 (2 dimensions)
Code units are specified in PL15
"""
# --------------------------------------
# Run settings
# --------------------------------------
boxres = [16, 56] # Low resolution test
#boxres = [32, 111] # Medium resolution test
#boxres = [64, 222] # High resolution test
nParticles = boxres[0] * boxres[1] # Must be specified
boxwidth = 0.5
hOverR = 0.05
R0 = 5. # code units
rho0 = 1e-3 # code units
intrinsicDustRho = 3. # in g/cm^3
dustSize = 1. # in mm
numOrbitsRun = 50.
dustFrac = 0.099
# --------------------------------------
# General settings
# --------------------------------------
# Generate a stretched cubic grid as a starting point
initialSnapKind = 'hexagonal'
initialFileName = 'hexgrid.std'
# See diskpy for info on changa presets
changaPreset = 'default'
verbose = False
# --------------------------------------
# Algorithm settings
# --------------------------------------
#damping = None # automatically set damping force
damping = 0.03 # price and laibe setting
# Sound crossing times to settle gas for
# Price and Laibe use 1000, but you can get away with less, probably
tGasSettle = 1000
# how many runs to settle for (zeroing velocity each time)
nRuns = 1
# For all the runs, how many neighbors to use for smoothing
nSmooth = 28 # PL15 use an "effective" neighbor number of about 28.3
|
ibackus/testdust
|
src/examples/settling-ICgen/settings_hexagonal.py
|
Python
|
mit
| 2,001
|
[
"Gaussian"
] |
f969d380861cabef1f8585b885116033fabc7ddd6b9954f66f4df60391acaffe
|
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""This sample checks if particles or a polymer added to the system obey(s) constraints."""
from __future__ import print_function
import espressomd
# Check if necessary features have been compiled
#############################################################
required_features = ["LENNARD_JONES"]
espressomd.assert_features(required_features)
from espressomd import thermostat
from espressomd import interactions
from espressomd import shapes
from espressomd import polymer
import numpy as np
# System parameters
#############################################################
system = espressomd.System(box_l=[50.0, 50.0, 50.0])
system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
np.random.seed(seed=system.seed)
# if no seed is provided espresso generates a seed
system.time_step = 0.01
system.cell_system.skin = 10.0
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
system.cell_system.set_n_square(use_verlet_lists=False)
system.non_bonded_inter[0, 0].lennard_jones.set_params(
epsilon=1, sigma=1,
cutoff=2**(1. / 6), shift="auto")
num_part = 30
# create random positions in the box sufficiently away from the walls
ran_pos = np.random.uniform(low=1, high=49, size=(num_part, 3))
system.part.add(id=np.arange(num_part),
pos=ran_pos, type=np.zeros(num_part, dtype=int))
# bottom wall, normal pointing in the +z direction, laid at z=0.1
floor = shapes.Wall(normal=[0, 0, 1], dist=0.1)
c1 = system.constraints.add(
particle_type=0, penetrable=False, only_positive=False, shape=floor)
# top wall, normal pointing in the -z direction, laid at z=49.9, since the
# normal direction points down, dist is -49.9
ceil = shapes.Wall(normal=[0, 0, -1], dist=-49.9)
c2 = system.constraints.add(
particle_type=0, penetrable=False, only_positive=False, shape=ceil)
# create_polymer will avoid violating the contraints
fene = interactions.FeneBond(k=30, d_r_max=2)
system.bonded_inter.add(fene)
# start it next to the wall to test it!
start = np.array([1, 1, 1])
# polymer.create_polymer(N_P=1, bond_length=1.0, MPC=50,
# start_id=num_part, start_pos=start, type_poly_neutral=0,
# type_poly_charged=0, bond=fene, constraints=1)
# Warmup
#############################################################
warm_steps = 200
warm_n_times = 100
min_dist = 0.9
lj_cap = 5
system.force_cap = lj_cap
i = 0
act_min_dist = system.analysis.min_dist()
system.thermostat.set_langevin(kT=0.0, gamma=1.0)
# warmp with zero temperature to remove overlaps
while (act_min_dist < min_dist or c1.min_dist() < min_dist or c2.min_dist() < min_dist):
for j in range(warm_steps + lj_cap):
print(j)
system.integrator.run(1)
# system.integrator.run(warm_steps + lj_cap)
# Warmup criterion
act_min_dist = system.analysis.min_dist()
i += 1
lj_cap = lj_cap + 1
system.force_cap = lj_cap
lj_cap = 0
system.force_cap = lj_cap
system.integrator.run(warm_steps)
# ramp up to simulation temperature
temp = 0
while (temp < 1.0):
system.thermostat.set_langevin(kT=temp, gamma=1.0)
system.integrator.run(warm_steps)
temp += 0.1
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
system.integrator.run(warm_steps)
for t in range(300):
system.integrator.run(1000)
# print the position to see if it stays within imposed constraints
print(system.part[0].pos)
|
hmenke/espresso
|
samples/constraints.py
|
Python
|
gpl-3.0
| 4,048
|
[
"ESPResSo"
] |
36a488bd5ee8aa6a8c8e786e6518c925112c4a93646838a8ea700ed09d84438f
|
from __future__ import absolute_import
from __future__ import print_function
import glob
import os, sys
from datetime import datetime, timedelta
import logging
log = logging.getLogger(__name__)
log.addHandler(logging.NullHandler())
import numpy as np
from .density_to_files import (accumulate_points_on_grid,
accumulate_points_on_grid_sdev, accumulate_energy_on_grid,
accumulate_points_on_grid_3d, accumulate_points_on_grid_sdev_3d,
accumulate_energy_on_grid_3d,
point_density, extent_density, point_density_3d, extent_density_3d, project,
flashes_to_frames, flash_count_log, extract_events_for_flashes)
from lmatools.stream.subset import broadcast
from lmatools.io.LMA_h5_file import read_flashes, to_seconds
from lmatools.coordinateSystems import MapProjection, GeographicSystem
from .cf_netcdf import (write_cf_netcdf, write_cf_netcdf_3d,
write_cf_netcdf_latlon, write_cf_netcdf_3d_latlon,
write_cf_netcdf_noproj, write_cf_netcdf_fixedgrid)
def dlonlat_at_grid_center(ctr_lat, ctr_lon, dx=4.0e3, dy=4.0e3,
x_bnd = (-100e3, 100e3), y_bnd = (-100e3, 100e3),
proj_datum = 'WGS84', proj_ellipse = 'WGS84'):
"""
Utility function useful for producing a regular grid of lat/lon data,
where an approximate spacing (dx, dy) and total span of the grid (x_bnd, y_bnd)
is desired. Units are in meters.
There is guaranteed to be distortion away from the grid center, i.e.,
only the grid cells adjacent to the center location will have area dx * dy.
Likewise, the lat, lon range is calculated naively using dlat, dlon multiplied
by the number of grid cells implied by x_bnd/dx, y_bnd/dy. This is the naive approach,
but probably what's expected when specifying distances in kilometers for
an inherently distorted lat/lon grid.
Returns:
(dlon, dlat, lon_bnd, lat_bnd)
corresponding to
(dx, dy, x_range, y_range)
"""
# Use the Azimuthal equidistant projection as the method for converting to kilometers.
proj_name = 'aeqd'
mapProj = MapProjection(projection=proj_name, ctrLat=ctr_lat, ctrLon=ctr_lon, lat_ts=ctr_lat,
lon_0=ctr_lon, lat_0=ctr_lat, lat_1=ctr_lat, ellipse=proj_ellipse, datum=proj_datum)
geoProj = GeographicSystem()
# Get dlat
lon_n, lat_n, z_n = geoProj.fromECEF(*mapProj.toECEF(0,dy,0))
dlat = lat_n - ctr_lat
# Get dlon
lon_e, lat_e, z_e = geoProj.fromECEF(*mapProj.toECEF(dx,0,0))
dlon = lon_e - ctr_lon
lon_min = ctr_lon + dlon * (x_bnd[0]/dx)
lon_max = ctr_lon + dlon * (x_bnd[1]/dx)
lat_min = ctr_lat + dlat * (y_bnd[0]/dy)
lat_max = ctr_lat + dlat * (y_bnd[1]/dy)
# Alternate method: lat lon for the actual distance to the NSEW in the projection
#lon_range_n, lat_range_n, z_range_n = geoProj.fromECEF(*mapProj.toECEF(0,y_bnd,0))
#lon_range_e, lat_range_e, z_range_e = geoProj.fromECEF(*mapProj.toECEF(x_bnd,0,0))
return dlon, dlat, (lon_min, lon_max), (lat_min, lat_max)
def time_edges(start_time, end_time, frame_interval):
""" Return lists cooresponding the start and end times of frames lasting frame_interval
between start_time and end_time. The last interval may extend beyond end_time, but
by no more than frame_interval. This makes each frame the same length.
returns t_edges, duration, where t_edges is a list of datetime objects, and
duration is the total duration between the start and end times (and not the duration
of all frames)
"""
frame_dt = timedelta(0, frame_interval, 0)
duration = end_time - start_time
n_frames = int(np.ceil(to_seconds(duration) / to_seconds(frame_dt)))
t_edges = [start_time + i*frame_dt for i in range(n_frames+1)]
return t_edges, duration
def seconds_since_start_of_day(start_time, t):
""" For each datetime object t, return the number of seconds elapsed since the
start of the date given by start_time. Only the date part of start_time is used.
"""
ref_date = start_time.date()
t_ref = datetime(ref_date.year, ref_date.month, ref_date.day)
t_edges_seconds = [to_seconds(edge - t_ref) for edge in t]
return t_ref, t_edges_seconds
class FlashGridder(object):
def __init__(self, start_time, end_time, do_3d = True,
frame_interval=120.0, dx=4.0e3, dy=4.0e3, dz=1.0e3,
base_date = None,
x_bnd = (-100e3, 100e3),
y_bnd = (-100e3, 100e3),
z_bnd = (0e3, 20e3),
ctr_lat = 35.23833, ctr_lon = -97.46028, ctr_alt=0.0,
proj_name = 'aeqd',
proj_datum = 'WGS84',
proj_ellipse = 'WGS84',
pixel_coords = None,
flash_count_logfile = None, energy_grids = None,
event_grid_area_fraction_key = None,
spatial_scale_factor = 1.0/1000.0,
subdivide=False,
):
""" Class to support gridding of flash and event data.
On init, specify the grid
If proj_name = 'pixel_grid' then pixel_coords must be an
instance of lmatools.coordinateSystems.PixelGrid
If proj_name = 'geos' then pixel_coords must be an instance of
lmatools.coordinateSystems.GeostationaryFixedGridSystem
energy_grids controls which energy grids are saved, default None.
energy_grids may be True, which will calculate all energy grid
types, or it may be one of 'specific_energy', 'total_energy',
or a list of one or more of these.
event_grid_area_fraction_key specifies the name of the variable
in the events array that gives the fraction of each grid cell
covered by each event. Used only for pixel-based event
detectors.
"""
if energy_grids == True:
energy_grids = ('specific_energy', 'total_energy')
self.energy_grids = energy_grids
self.spatial_scale_factor = spatial_scale_factor
self.event_grid_area_fraction_key = event_grid_area_fraction_key
# args, kwargs that are saved for the future
self.do_3d = do_3d
self.start_time = start_time
self.dx, self.dy, self.dz = dx, dy, dz
self.end_time = end_time
self.frame_interval = frame_interval
self.base_date = base_date
self.min_points_per_flash = 1
self.proj_name = proj_name
self.ctr_lat, self.ctr_lon, self.ctr_alt = ctr_lat, ctr_lon, ctr_alt
if flash_count_logfile is None:
flash_count_logfile = log
self.flash_count_logfile = flash_count_logfile
t_edges, duration = time_edges(self.start_time, self.end_time, self.frame_interval)
# reference time is the date part of the start_time, unless the user provides a different date.
if self.base_date is None:
t_ref, t_edges_seconds = seconds_since_start_of_day(self.start_time, t_edges)
else:
t_ref, t_edges_seconds = seconds_since_start_of_day(self.base_date, t_edges)
self.n_frames = len(t_edges)-1
xedge=np.arange(x_bnd[0], x_bnd[1]+dx, dx)
yedge=np.arange(y_bnd[0], y_bnd[1]+dy, dy)
zedge=np.arange(z_bnd[0], z_bnd[1]+dz, dz)
if self.proj_name == 'latlong':
dx_units = '{0:6.4f}deg'.format(float(dx))
mapProj = GeographicSystem()
elif self.proj_name == 'pixel_grid':
dx_units = 'pixel'
mapProj = pixel_coords
elif self.proj_name == 'geos':
dx_units = '{0:03d}urad'.format(int(dx*1e6))
mapProj = pixel_coords
else:
dx_units = '{0:5.1f}m'.format(float(dx))
mapProj = MapProjection(projection=self.proj_name, ctrLat=ctr_lat, ctrLon=ctr_lon, lat_ts=ctr_lat,
lon_0=ctr_lon, lat_0=ctr_lat, lat_1=ctr_lat, ellipse=proj_ellipse, datum=proj_datum)
geoProj = GeographicSystem()
self.t_ref = t_ref
self.t_edges = t_edges
self.t_edges_seconds = t_edges_seconds
self.duration = duration
self.xedge = xedge
self.yedge = yedge
self.zedge = zedge
self.mapProj = mapProj
self.geoProj = geoProj
self.dx_units = dx_units
self.pipeline_setup()
self.output_setup()
def pipeline_setup(self):
"""
Create the grids for each variable of interest.
Set up the data processing pipeline up to the point at which data are
written to grids in memory.
"""
event_grid_area_fraction_key=self.event_grid_area_fraction_key
energy_grids=self.energy_grids
n_frames = self.n_frames
xedge, yedge, zedge = self.xedge, self.yedge, self.zedge
dx, dy, dz = self.dx, self.dy, self.dz
x0 = xedge[0]
y0 = yedge[0]
z0 = zedge[0]
mapProj = self.mapProj
geoProj = self.geoProj
event_density_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='int32')
init_density_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='int32')
if self.event_grid_area_fraction_key is not None:
extent_density_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='float32')
else:
extent_density_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='int32')
footprint_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='float32')
specific_energy_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='float32')
total_energy_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='float32')
flashsize_std_grid = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, n_frames), dtype='float32')
if self.do_3d == True:
event_density_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='int32')
init_density_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='int32')
extent_density_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='int32')
footprint_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='float32')
specific_energy_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='float32')
total_energy_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='float32')
flashsize_std_grid_3d = np.zeros((xedge.shape[0]-1, yedge.shape[0]-1, zedge.shape[0]-1, n_frames), dtype='float32')
self.outgrids = (extent_density_grid,
init_density_grid,
event_density_grid,
footprint_grid,
specific_energy_grid,
flashsize_std_grid,
total_energy_grid,
)
if self.do_3d == True:
self.outgrids_3d = (extent_density_grid_3d,
init_density_grid_3d,
event_density_grid_3d,
footprint_grid_3d,
specific_energy_grid_3d,
flashsize_std_grid_3d,
total_energy_grid_3d
)
else:
self.outgrids_3d = None
all_frames = []
for i in range(n_frames):
extent_out = {'name':'extent'}
init_out = {'name':'init'}
event_out = {'name':'event'}
std_out = {'name':'std'}
extent_out_3d = {'name':'extent_3d'}
init_out_3d = {'name':'init_3d'}
event_out_3d = {'name':'event_3d'}
std_out_3d = {'name':'std_3d'}
accum_event_density = accumulate_points_on_grid(event_density_grid[:,:,i], xedge, yedge, out=event_out, label='event')
accum_init_density = accumulate_points_on_grid(init_density_grid[:,:,i], xedge, yedge, out=init_out, label='init')
accum_extent_density = accumulate_points_on_grid(extent_density_grid[:,:,i], xedge, yedge, out=extent_out,label='extent', grid_frac_weights=True)
accum_footprint = accumulate_points_on_grid(footprint_grid[:,:,i], xedge, yedge, label='footprint', grid_frac_weights=True)
accum_specific_energy = accumulate_energy_on_grid(specific_energy_grid[:,:,i], xedge, yedge, out=extent_out, label='specific_energy', grid_frac_weights=True)
accum_flashstd = accumulate_points_on_grid_sdev(flashsize_std_grid[:,:,i], footprint_grid[:,:,i], xedge, yedge, out=extent_out, label='flashsize_std', grid_frac_weights=True)
accum_total_energy = accumulate_energy_on_grid(total_energy_grid[:,:,i], xedge, yedge, out=extent_out, label='total_energy', grid_frac_weights=True)
if self.do_3d == True:
accum_event_density_3d = accumulate_points_on_grid_3d(event_density_grid_3d[:,:,:,i], xedge, yedge, zedge, out=event_out_3d, label='event_3d')
accum_init_density_3d = accumulate_points_on_grid_3d(init_density_grid_3d[:,:,:,i], xedge, yedge, zedge, out=init_out_3d, label='init_3d')
accum_extent_density_3d = accumulate_points_on_grid_3d(extent_density_grid_3d[:,:,:,i], xedge, yedge, zedge, out=extent_out_3d,label='extent_3d')
accum_footprint_3d = accumulate_points_on_grid_3d(footprint_grid_3d[:,:,:,i], xedge, yedge, zedge, label='footprint_3d')
accum_specific_energy_3d = accumulate_energy_on_grid_3d(specific_energy_grid_3d[:,:,:,i], xedge, yedge, zedge, out=extent_out_3d,label='specific_energy_3d')
accum_flashstd_3d = accumulate_points_on_grid_sdev_3d(flashsize_std_grid_3d[:,:,:,i], footprint_grid_3d[:,:,:,i], xedge, yedge, zedge, out=extent_out_3d,label='flashsize_std_3d')
accum_total_energy_3d = accumulate_energy_on_grid_3d(total_energy_grid_3d[:,:,:,i], xedge, yedge, zedge, out=extent_out_3d,label='total_energy_3d')
extent_out['func'] = accum_extent_density
init_out['func'] = accum_init_density
event_out['func'] = accum_event_density
if self.do_3d == True:
extent_out_3d['func'] = accum_extent_density_3d
init_out_3d['func'] = accum_init_density_3d
event_out_3d['func'] = accum_event_density_3d
event_density_target = point_density(accum_event_density)
init_density_target = point_density(accum_init_density)
extent_density_target = extent_density(x0, y0, dx, dy, accum_extent_density,
event_grid_area_fraction_key=event_grid_area_fraction_key)
mean_footprint_target = extent_density(x0, y0, dx, dy, accum_footprint, weight_key='area',
event_grid_area_fraction_key=event_grid_area_fraction_key)
mean_energy_target = extent_density(x0, y0, dx, dy, accum_specific_energy, weight_key='specific_energy',
event_grid_area_fraction_key=event_grid_area_fraction_key)
mean_total_energy_target = extent_density(x0, y0, dx, dy, accum_total_energy, weight_key='total_energy',
event_grid_area_fraction_key=event_grid_area_fraction_key)
std_flashsize_target = extent_density(x0, y0, dx, dy, accum_flashstd, weight_key='area',
event_grid_area_fraction_key=event_grid_area_fraction_key)
if self.do_3d == True:
event_density_target_3d = point_density_3d(accum_event_density_3d)
init_density_target_3d = point_density_3d(accum_init_density_3d)
extent_density_target_3d = extent_density_3d(x0, y0, z0, dx, dy, dz, accum_extent_density_3d)
mean_footprint_target_3d = extent_density_3d(x0, y0, z0, dx, dy, dz, accum_footprint_3d, weight_key='area')
mean_energy_target_3d = extent_density_3d(x0, y0, z0, dx, dy, dz, accum_specific_energy_3d, weight_key='specific_energy')
mean_total_energy_target_3d = extent_density_3d(x0, y0, z0, dx, dy, dz, accum_total_energy_3d, weight_key='total_energy')
std_flashsize_target_3d = extent_density_3d(x0, y0, z0, dx, dy, dz, accum_flashstd_3d, weight_key='area')
broadcast_targets = (
project('lon', 'lat', 'alt', mapProj, geoProj, event_density_target, use_flashes=False),
project('init_lon', 'init_lat', 'init_alt', mapProj, geoProj, init_density_target, use_flashes=True),
project('lon', 'lat', 'alt', mapProj, geoProj, extent_density_target, use_flashes=False),
project('lon', 'lat', 'alt', mapProj, geoProj, mean_footprint_target, use_flashes=False),
project('lon', 'lat', 'alt', mapProj, geoProj, std_flashsize_target, use_flashes=False),
)
if energy_grids is not None:
if ('specific_energy' == energy_grids) | ('specific_energy' in energy_grids):
broadcast_targets += (
project('lon', 'lat', 'alt', mapProj, geoProj, mean_energy_target, use_flashes=False),
)
if ('total_energy' == energy_grids) | ('total_energy' in energy_grids):
broadcast_targets += (
project('lon', 'lat', 'alt', mapProj, geoProj, mean_total_energy_target, use_flashes=False),
)
if self.do_3d == True:
broadcast_targets += (
project('lon', 'lat', 'alt', mapProj, geoProj, event_density_target_3d, use_flashes=False),
project('init_lon', 'init_lat', 'init_alt', mapProj, geoProj, init_density_target_3d, use_flashes=True),
project('lon', 'lat', 'alt', mapProj, geoProj, extent_density_target_3d, use_flashes=False),
project('lon', 'lat', 'alt', mapProj, geoProj, mean_footprint_target_3d, use_flashes=False),
project('lon', 'lat', 'alt', mapProj, geoProj, std_flashsize_target_3d, use_flashes=False),
)
if energy_grids is not None:
if ('specific_energy' == energy_grids) | ('specific_energy' in energy_grids):
broadcast_targets += (
project('lon', 'lat', 'alt', mapProj, geoProj, mean_energy_target_3d, use_flashes=False),
)
if ('total_energy' == energy_grids) | ('total_energy' in energy_grids):
broadcast_targets += (
project('lon', 'lat', 'alt', mapProj, geoProj, mean_total_energy_target_3d, use_flashes=False),
)
spew_to_density_types = broadcast( broadcast_targets )
all_frames.append( extract_events_for_flashes( spew_to_density_types ) )
frame_count_log = flash_count_log(self.flash_count_logfile)
framer = flashes_to_frames(self.t_edges_seconds, all_frames,
time_key='start', time_edges_datetime=self.t_edges,
flash_counter=frame_count_log)
self.framer=framer
def output_setup(self):
"""
For each of the grids of interest in self.outgrids, set up the
outfile names, units, etc. These are all the metadata that go with the
actual values on the grids.
"""
energy_grids = self.energy_grids
spatial_scale_factor = self.spatial_scale_factor
dx, dy, dz = self.dx, self.dy, self.dz
self.outfile_postfixes = ('flash_extent.nc',
'flash_init.nc',
'source.nc',
'footprint.nc',
'specific_energy.nc',
'flashsize_std.nc',
'total_energy.nc')
self.outfile_postfixes_3d = ('flash_extent_3d.nc',
'flash_init_3d.nc',
'source_3d.nc',
'footprint_3d.nc',
'specific_energy_3d.nc',
'flashsize_std_3d.nc',
'total_energy_3d.nc')
self.field_names = ('flash_extent',
'flash_initiation',
'lma_source',
'flash_footprint',
'specific_energy',
'flashsize_std',
'total_energy')
self.field_descriptions = ('LMA flash extent density',
'LMA flash initiation density',
'LMA source density',
'LMA local mean flash area',
'LMA flash specific energy (approx)',
'LMA local standard deviation of flash size',
'LMA flash total energy (approx)')
# In some use cases, it's easier to calculate totals (for area or
# energy) and then divide at the end. This dictionary maps numerator
# to denominator, with an index corresponding to self.outgrids.
# The avearge is then calculated on output with numerator_out =
# numerator/denominator. For example to calculate average energy
# instead of total energy:
# self.divide_grids[6]=0
# and change the labels in field_names, etc. to read as averages
# instead of totals.
self.divide_grids = {}
if self.proj_name=='latlong':
density_units = "grid"
density_units_3d = "grid"
else:
density_units = "{0:5.1f} km^2".format(dx*spatial_scale_factor * dy*spatial_scale_factor).lstrip()
density_units_3d = "{0:5.1f} km^3".format(dx*spatial_scale_factor * dy*spatial_scale_factor * dz*spatial_scale_factor).lstrip()
time_units = "{0:5.1f} min".format(self.frame_interval/60.0).lstrip()
density_label = 'Count per ' + density_units + " pixel per "+ time_units
density_label_3d = 'Count per ' + density_units_3d + " pixel per "+ time_units
self.field_units = ( density_label,
density_label,
density_label,
"km^2 per flash",
"J/kg per flash",
density_label,
"J per flash",
)
self.field_units_3d = ( density_label_3d,
density_label_3d,
density_label_3d,
"km^2 per flash",
"J/kg per flash",
density_label_3d,
"J per flash",
)
if self.event_grid_area_fraction_key is not None:
extent_format='f'
else:
extent_format='i'
self.outformats = tuple((extent_format, 'i', 'i', 'f', 'f', 'f', 'f'))
self.outformats_3d = tuple((extent_format, 'i', 'i', 'f', 'f', 'f', 'f'))
remove_idx = []
if energy_grids is not None:
if ('specific_energy' == energy_grids) | ('specific_energy' in energy_grids):
pass #keep index 4
else:
remove_idx.append(4)
if ('total_energy' == energy_grids) | ('total_energy' in energy_grids):
pass # keep index 6
else:
remove_idx.append(6)
# Remove indices above so they're not written.
def filter_energy(var):
for i, k in enumerate(var):
if i not in remove_idx:
yield k
self.outgrids = tuple(k for k in filter_energy(self.outgrids))
self.outfile_postfixes = tuple(k for k in
filter_energy(self.outfile_postfixes))
self.field_names = tuple(k for k in filter_energy(self.field_names))
self.field_units = tuple(k for k in filter_energy(self.field_units))
self.field_descriptions = tuple(k for k in
filter_energy(self.field_descriptions))
self.outformats = tuple(k for k in filter_energy(self.outformats))
if self.do_3d:
self.outgrids_3d = tuple(k for k in filter_energy(self.outgrids_3d))
self.outfile_postfixes_3d = tuple(k for k in
filter_energy(self.outfile_postfixes_3d))
self.field_units_3d = tuple(k for k in filter_energy(self.field_units_3d))
self.outformats_3d = tuple(k for k in filter_energy(self.outformats_3d))
def write_grids(self, outpath = '', output_writer = write_cf_netcdf,
output_writer_3d = write_cf_netcdf_3d,
calculate_2D_lonlat=True,
output_filename_prefix="LMA", output_kwargs = {}):
spatial_scale_factor = self.spatial_scale_factor
xedge = self.xedge
yedge = self.yedge
zedge = self.zedge
t_ref = self.t_ref
t_edges_seconds = self.t_edges_seconds
mapProj = self.mapProj
geoProj = self.geoProj
outgrids = self.outgrids
outgrids_3d = self.outgrids_3d
x_coord = (xedge[:-1] + xedge[1:])/2.0
y_coord = (yedge[:-1] + yedge[1:])/2.0
z_coord = (zedge[:-1] + zedge[1:])/2.0
nx = x_coord.shape[0]
ny = y_coord.shape[0]
nz = z_coord.shape[0]
x_all, y_all = (a.T for a in np.meshgrid(x_coord, y_coord))
assert x_all.shape == y_all.shape
assert x_all.shape[0] == nx
assert x_all.shape[1] == ny
z_all = np.zeros_like(x_all)
if calculate_2D_lonlat:
log.info("Calculating dense 2D lon lat grid from x y z")
lons, lats, alts = x,y,z = geoProj.fromECEF( *mapProj.toECEF(x_all, y_all, z_all) )
lons.shape=x_all.shape
lats.shape=y_all.shape
else:
lons = None
lats = None
alts = None
x = None
y = None
z = None
basename_parts = (output_filename_prefix,
self.start_time.strftime('%Y%m%d_%H%M%S'),
to_seconds(self.duration),
self.min_points_per_flash,
self.dx_units,
)
outfile_template = '%s_%s_%d_%dsrc_%s-dx_%s'
outfile_basenames = list(outfile_template % (basename_parts + (pfx,))
for pfx in self.outfile_postfixes)
outfiles = list(os.path.join(outpath, outfile_basename)
for outfile_basename in outfile_basenames)
if self.do_3d:
grid_shape_3d = (nx,ny,nz)
x_ones_3d = np.ones(grid_shape_3d, dtype='f4')
y_ones_3d = np.ones(grid_shape_3d, dtype='f4')
z_ones_3d = np.ones(grid_shape_3d, dtype='f4')
x_all_3d = x_coord[:, None, None]*x_ones_3d
y_all_3d = y_coord[None,:,None]*y_ones_3d
z_all_3d = z_coord[None, None, :]*z_ones_3d
lons_3d, lats_3d, alts_3d = x_3d,y_3d,z_3d = geoProj.fromECEF(*mapProj.toECEF(x_all_3d, y_all_3d, z_all_3d) )
lons_3d.shape=x_all_3d.shape
lats_3d.shape=y_all_3d.shape
alts_3d.shape=z_all_3d.shape
outfile_basenames_3d = (outfile_template % (basename_parts + (pfx,))
for pfx in self.outfile_postfixes_3d)
outfile_basenames_3d = list(outfile_basenames_3d)
outfiles_3d = (os.path.join(outpath, outfile_basename)
for outfile_basename in outfile_basenames_3d)
outfiles_3d = list(outfiles_3d)
file_iter = list(zip(
outfiles, self.outgrids, self.field_names,
self.field_descriptions, self.field_units, self.outformats))
for i, (outfile, grid, field_name, description, units, outformat) in enumerate(file_iter):
if i in self.divide_grids:
denom = self.outgrids[self.divide_grids[i]]
zeros = (denom == 0) | (grid == 0)
grid = grid/denom
grid[zeros] = 0 # avoid nans
log.info("Preparing to write NetCDF %s".format(outfile))
output_writer(outfile, t_ref, np.asarray(t_edges_seconds[:-1]),
x_coord*spatial_scale_factor,
y_coord*spatial_scale_factor,
lons, lats, self.ctr_lat, self.ctr_lon,
grid, field_name, description,
format=outformat, grid_units=units,
**output_kwargs)
########3D:
if self.outgrids_3d is not None:
for (outfile, grid, field_name, description, units, outformat) in zip(
outfiles_3d, self.outgrids_3d, self.field_names,
self.field_descriptions, self.field_units_3d,
self.outformats_3d):
output_writer_3d(outfile, t_ref,
np.asarray(t_edges_seconds[:-1]),
x_coord*spatial_scale_factor,
y_coord*spatial_scale_factor,
z_coord*spatial_scale_factor,
lons_3d, lats_3d, alts_3d,
self.ctr_lat, self.ctr_lon, self.ctr_alt,
grid, field_name, description,
format=outformat, grid_units=units,
**output_kwargs)
def process_flashes(self, h5_filenames, min_points_per_flash=10):
self.min_points_per_flash = min_points_per_flash
read_flashes( h5_filenames, self.framer, base_date=self.t_ref, min_points=min_points_per_flash)
def grid_h5flashfiles(h5_filenames, start_time, end_time, **kwargs):
""" Grid LMA data contianed in HDF5-format LMA files. Keyword arguments to this function
are those to the FlashGridder class and its functions.
This function is provided as a convenience for compatibility with earlier
implementations of flash gridding.
"""
process_flash_kwargs = {}
for prock in ('min_points_per_flash',):
if prock in kwargs:
process_flash_kwargs[prock] = kwargs.pop(prock)
out_kwargs = {}
for outk in ('outpath', 'output_writer', 'output_writer_3d',
'output_kwargs', 'output_filename_prefix'):
if outk in kwargs:
out_kwargs[outk] = kwargs.pop(outk)
gridder = FlashGridder(start_time, end_time, **kwargs)
gridder.process_flashes(h5_filenames, **process_flash_kwargs)
output = gridder.write_grids(**out_kwargs)
return output
if __name__ == '__main__':
h5_filenames = glob.glob('data/LYL*090610_20*.h5')
start_time = datetime(2009,6,10, 20,0,0)
end_time = datetime(2009,6,10, 21,0,0)
frame_interval=120.0
dx=4.0e3
dy=4.0e3
x_bnd = (-100e3, 100e3)
y_bnd = (-100e3, 100e3)
# # KOUN
ctr_lat = 35.23833
ctr_lon = -97.46028
# DC
# ctr_lat = 38.889444
# ctr_lon = -77.035278
grid_h5flashfiles(h5_filenames, start_time, end_time, frame_interval=frame_interval,
dx=dx, dy=dy, x_bnd=x_bnd, y_bnd=y_bnd, ctr_lon=ctr_lon, ctr_lat=ctr_lat)
|
deeplycloudy/lmatools
|
lmatools/grid/make_grids.py
|
Python
|
bsd-2-clause
| 31,955
|
[
"NetCDF"
] |
95a5467961712e9dc67c865d3d6f9265d10b3f4febe43cd32000ade8acd5950d
|
# This file is part of BHMM (Bayesian Hidden Markov Models).
#
# Copyright (c) 2016 Frank Noe (Freie Universitaet Berlin)
# and John D. Chodera (Memorial Sloan-Kettering Cancer Center, New York)
#
# BHMM is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import numpy as np
from bhmm.hmm.generic_hmm import HMM
from bhmm.hmm.generic_sampled_hmm import SampledHMM
from bhmm.output_models.discrete import DiscreteOutputModel
from bhmm.util import config
from bhmm.util.statistics import confidence_interval_arr
class DiscreteHMM(HMM, DiscreteOutputModel):
r""" Convenience access to an HMM with a Gaussian output model.
"""
def __init__(self, hmm):
# superclass constructors
if not isinstance(hmm.output_model, DiscreteOutputModel):
raise TypeError('Given hmm is not a discrete HMM, but has an output model of type: ' +
str(type(hmm.output_model)))
DiscreteOutputModel.__init__(self, hmm.output_model.output_probabilities)
HMM.__init__(self, hmm.initial_distribution, hmm.transition_matrix, self, lag=hmm.lag)
class SampledDiscreteHMM(DiscreteHMM, SampledHMM):
""" Sampled Discrete HMM with a representative single point estimate and error estimates
Parameters
----------
estimated_hmm : :class:`HMM <generic_hmm.HMM>`
Representative HMM estimate, e.g. a maximum likelihood estimate or mean HMM.
sampled_hmms : list of :class:`HMM <generic_hmm.HMM>`
Sampled HMMs
conf : float, optional, default = 0.95
confidence interval, e.g. 0.68 for 1 sigma or 0.95 for 2 sigma.
"""
def __init__(self, estimated_hmm, sampled_hmms, conf=0.95):
# call GaussianHMM superclass constructer with estimated_hmm
DiscreteHMM.__init__(self, estimated_hmm)
# call SampledHMM superclass constructor
SampledHMM.__init__(self, estimated_hmm, sampled_hmms, conf=conf)
@property
def output_probabilities_samples(self):
r""" Samples of the output probability matrix """
res = np.empty((self.nsamples, self.nstates, self.dimension), dtype=config.dtype)
for i in range(self.nsamples):
res[i, :, :] = self._sampled_hmms[i].means
return res
@property
def output_probabilities_mean(self):
r""" The mean of the output probability matrix """
return np.mean(self.output_probabilities_samples, axis=0)
@property
def output_probabilities_std(self):
r""" The standard deviation of the output probability matrix """
return np.std(self.output_probabilities_samples, axis=0)
@property
def output_probabilities_conf(self):
r""" The standard deviation of the output probability matrix """
return confidence_interval_arr(self.output_probabilities_samples, conf=self._conf)
|
jchodera/bhmm
|
bhmm/hmm/discrete_hmm.py
|
Python
|
lgpl-3.0
| 3,417
|
[
"Gaussian"
] |
81d28d8b33685670517b2cc375e9be7aee18609eac805514cd2a0da0ab82d2c6
|
#!/usr/bin/env python
"""
Restart DIRAC component using runsvctrl utility
"""
__RCSID__ = "$Id$"
#
from DIRAC.Core.Base import Script
Script.disableCS()
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgfile] ... [System [Service|Agent]]' % Script.scriptName,
'Arguments:',
' System: Name of the system for the component (default *: all)',
' Service|Agent: Name of the particular component (default *: all)']))
Script.parseCommandLine()
args = Script.getPositionalArgs()
if len(args) > 2:
Script.showHelp()
exit(-1)
system = '*'
component = '*'
if args:
system = args[0]
if system != '*':
if len(args) > 1:
component = args[1]
#
from DIRAC.FrameworkSystem.Client.ComponentInstaller import gComponentInstaller
#
gComponentInstaller.exitOnError = True
#
result = gComponentInstaller.runsvctrlComponent(system, component, 't')
if not result['OK']:
print 'ERROR:', result['Message']
exit(-1)
gComponentInstaller.printStartupStatus(result['Value'])
|
andresailer/DIRAC
|
FrameworkSystem/scripts/dirac-restart-component.py
|
Python
|
gpl-3.0
| 1,178
|
[
"DIRAC"
] |
1849798b4ac541bef98b76240f0bf7aebc9b4043db30090463db9a15467c3039
|
"""Script to download or update SIMBAD-related databases"""
__author__ = "Felix Simkovic & Adam Simpkin"
__date__ = "17 May 2017"
__version__ = "1.0"
import argparse
import collections
import datetime
import glob
import json
import numpy as np
import pandas as pd
import morda
import os
import shutil
import ssl
import sys
import tarfile
import uuid
from distutils.version import StrictVersion
import pyjob
from pyjob.stopwatch import StopWatch
from pyjob.script import ScriptCollector, Script
import cctbx.crystal
import simbad
import simbad.command_line
import simbad.db
import simbad.exit
import simbad.rotsearch.amore_search
import simbad.util
import simbad.util.logging_util
from simbad.util import submit_chunk
from simbad.util import tmp_dir
from simbad.util.pdb_util import PdbStructure
if sys.version_info.major < 3:
from urllib2 import urlopen, HTTPError
from urllib import urlretrieve
else:
from urllib.error import HTTPError
from urllib.request import urlopen, urlretrieve
logger = None
# The space groups in the list below cannot be recognized by CCTBX, so we convert them
# to similar ones understandable by the library
CCTBX_ERROR_SG = {
'A1': 'P1',
'B2': 'B112',
'C1211': 'C2',
'F422': 'I422',
'I21': 'I2',
'I1211': 'I2',
'P21212A': 'P212121',
'R3': 'R3:R',
'C4212': 'P422',
}
SYS_PLATFORM = sys.platform
CUSTOM_PLATFORM = "linux" if SYS_PLATFORM in ["linux", "linux2"] \
else "mac" if SYS_PLATFORM in ["darwin"] \
else "windows"
if os.name != "nt":
if "SSL_CERT_FILE" not in os.environ:
os.environ["SSL_CERT_FILE"] = os.path.join(os.environ["CCP4"], 'etc', 'ssl', 'cacert.pem')
ContaminantSearchResult = collections.namedtuple("ContaminantSearchResult", ["pdb_code", "space_group", "uniprot_name", "uniprot_mnemonic"])
def is_valid_db_location(database):
"""Validate permissions for a database"""
return os.access(os.path.dirname(os.path.abspath(database)), os.W_OK)
def is_readable_file(file):
"""Validate that the PDB file is readable"""
try:
pdb_struct = PdbStructure().from_file(file)
# Call functions that require file to be properly read
assert pdb_struct.molecular_weight != 0
assert pdb_struct.nres != 0
except Exception:
return False
return True
def download_morda():
"""Download the MoRDa database
Returns
-------
str
The path to the downloaded MoRDa database
"""
logger.info("Downloading MoRDa database from CCP4")
url = "http://www.ccp4.ac.uk/morda/MoRDa_DB.tar.gz"
url_legacy = "http://legacy.ccp4.ac.uk/morda/MoRDa_DB.tar.gz"
local_db = os.path.basename(url)
# http://stackoverflow.com/a/34831866/3046533
chunk_size = 1 << 20
with open(local_db, "wb") as f_out:
try:
query = urlopen(url)
except HTTPError:
query = urlopen(url_legacy)
while True:
chunk = query.read(chunk_size)
if not chunk:
break
f_out.write(chunk)
with tarfile.open(local_db) as tar:
members = [
tarinfo for tarinfo in tar.getmembers()
if tarinfo.path.startswith("MoRDa_DB/home/ca_DOM") or tarinfo.path.startswith("MoRDa_DB/home/ca_DB")
or tarinfo.path.startswith("MoRDa_DB/pdb_DB_gz") or tarinfo.path.startswith(
"MoRDa_DB/" + "bin_" + CUSTOM_PLATFORM) or tarinfo.path.startswith("MoRDa_DB/list/domain_list.dat")
]
tar.extractall(members=members)
os.remove(local_db)
os.environ["MRD_DB"] = os.path.abspath("MoRDa_DB")
os.environ["MRD_PROG"] = os.path.join(os.path.abspath("MoRDa_DB"), "bin_" + CUSTOM_PLATFORM)
def create_lattice_db(database):
"""Create a lattice search database
Parameters
----------
database : str
The path to the database file
"""
if not is_valid_db_location(database):
raise RuntimeError("Permission denied! Cannot write to {}!".format(os.path.dirname(database)))
logger.info('Querying the PDBe Protein DataBank')
crystal_data, error_count = [], 0
url = 'https://www.ebi.ac.uk/pdbe/search/pdb/select?q=pdb_id:*' \
'&fq=experimental_method:"X-ray%20diffraction"&rows=1000000&fl=pdb_id,cell_alpha,cell_beta,cell_gamma,' \
'cell_a,cell_b,cell_c,spacegroup,experimental_method&wt=csv'
pdbe_report_file = os.path.join(os.environ["CCP4_SCR"], "pdbe_{}.csv".format(uuid.uuid1()))
ssl._create_default_https_context = ssl._create_unverified_context
urlretrieve(url, pdbe_report_file)
df = pd.read_csv(pdbe_report_file)
df = df.drop_duplicates()
df = df.dropna()
for index, row in df.iterrows():
pdb_code = row['pdb_id']
unit_cell = [row['cell_a'], row['cell_b'], row['cell_c'],
row['cell_alpha'], row['cell_beta'], row['cell_gamma']]
space_group = row['spacegroup'].replace(" ", "").strip()
space_group = CCTBX_ERROR_SG.get(space_group, space_group)
try:
symmetry = cctbx.crystal.symmetry(
unit_cell=unit_cell, space_group=space_group, correct_rhombohedral_setting_if_necessary=True)
except Exception as e:
logger.debug('Skipping pdb entry %s\t%s', pdb_code, e)
error_count += 1
continue
crystal_data.append((pdb_code, symmetry))
logger.debug('Error processing %d pdb entries', error_count)
if os.path.isfile(pdbe_report_file):
os.remove(pdbe_report_file)
logger.info('Calculating the Niggli cells')
niggli_data = np.zeros((len(crystal_data), 11))
# Leave this as list, .append is faster than .vstack
alt_niggli_data = []
for i, xtal_data in enumerate(crystal_data):
niggli_data[i][:4] = np.fromstring(xtal_data[0], dtype='uint8').astype(np.float64)
niggli_data[i][4] = ord('\x00')
niggli_data[i][5:] = np.array(xtal_data[1].niggli_cell().unit_cell().parameters()).round(decimals=3)
a, b, c, alpha, beta, gamma = niggli_data[i][5:]
# Add alternate niggli cell where a and b may be flipped
if np.allclose(a, b, atol=(b / 100.0 * 1.0)) and a != b and alpha != beta:
alt_niggli_data += [np.concatenate((niggli_data[i][:4], np.array([ord('*'), b, a, c, beta, alpha, gamma])))]
# Add alternate niggli cell where b and c may be flipped
if np.allclose(b, c, atol=(c / 100.0 * 1.0)) and b != c and beta != gamma:
alt_niggli_data += [np.concatenate((niggli_data[i][:4], np.array([ord('*'), a, c, b, alpha, gamma, beta])))]
niggli_data = np.vstack([niggli_data, np.asarray(alt_niggli_data)])
logger.info("Total Niggli cells loaded: %d", niggli_data.shape[0])
if not database.endswith('.npz'):
database += ".npz"
logger.info('Storing database in file: %s', database)
np.savez_compressed(database, niggli_data)
def create_contaminant_db(database, add_morda_domains, nproc=2, submit_qtype=None, submit_queue=False):
"""Create a contaminant database
Parameters
----------
database : str
The path to the database folder
add_morda_domains : bool
Retrospectively add morda domains to a contaminant database updated when morda was not installed
nproc : int, optional
The number of processors [default: 2]
submit_qtype : str
The cluster submission queue type - currently support SGE and LSF
submit_queue : str
The queue to submit to on the cluster
Raises
------
RuntimeError
dimple.contaminants.prepare module not available
RuntimeError
Windows is currently not supported
"""
if not is_valid_db_location(database):
raise RuntimeError("Permission denied! Cannot write to {}!".format(os.path.dirname(database)))
import dimple.main
logger.info('DIMPLE version: %s', dimple.main.__version__)
if CUSTOM_PLATFORM == "windows":
msg = "Windows is currently not supported"
raise RuntimeError(msg)
if StrictVersion(dimple.main.__version__) < StrictVersion('2.6.1'):
msg = "Downloading latest Contaminant database from GitHub repo"
logger.info(msg)
cmd = ['svn', 'export', 'https://github.com/rigdenlab/SIMBAD/trunk/static/contaminants']
try:
pyjob.cexec(cmd)
except:
msg = "Error downloading contaminant directory from https://github.com/rigdenlab/SIMBAD/trunk/static/contaminants"
raise RuntimeError(msg)
if os.path.isdir(database):
shutil.rmtree(database)
shutil.move(os.path.join(os.getcwd(), 'contaminants'), database)
return
import dimple.contaminants.prepare
dimple.contaminants.prepare.main(verbose=False)
simbad_dat_path = os.path.join(database, '*', '*', '*', '*.dat')
existing_dat_files = [os.path.basename(f).split('.')[0].lower() for f in glob.iglob(simbad_dat_path)]
erroneous_files = ['4v43']
dimple_files = ['cached', 'data.json', 'data.py']
with open("data.json") as data_file:
data = json.load(data_file)
results = []
for child in data["children"]:
try:
for child_2 in child["children"]:
space_group = child_2["name"].replace(" ", "")
for child_3 in child_2["children"]:
pdb_code = child_3["name"].split()[0].lower()
if (pdb_code in existing_dat_files or pdb_code in erroneous_files) and not add_morda_domains:
continue
uniprot_name = child["name"]
uniprot_mnemonic = uniprot_name.split('_')[1]
score = ContaminantSearchResult(pdb_code, space_group, uniprot_name, uniprot_mnemonic)
results.append(score)
except KeyError:
pass
if len(results) == 0:
logger.info("Contaminant database up to date")
else:
if add_morda_domains:
logger.info("Adding morda domains to contaminant database")
else:
logger.info("%d new entries were found in the contaminant database, " + "updating SIMBAD database",
len(results))
if "MRD_DB" in os.environ:
morda_installed_through_ccp4 = True
else:
morda_installed_through_ccp4 = False
if add_morda_domains and not morda_installed_through_ccp4:
logger.critical("Morda not installed locally, unable to add morda domains to contaminant database")
if morda_installed_through_ccp4:
morda_dat_path = os.path.join(os.environ['MRD_DB'], 'home', 'ca_DOM', '*.dat')
morda_dat_files = set([os.path.basename(f) for f in glob.iglob(morda_dat_path)])
exe = os.path.join(os.environ['MRD_PROG'], "get_model")
else:
logger.info(
"Morda not installed locally, therefore morda domains will not be added to contaminant database")
files = []
collector = ScriptCollector(None)
for result in results:
stem = os.path.join(os.getcwd(), database, result.uniprot_mnemonic, result.uniprot_name, result.space_group)
if not os.path.exists(stem):
os.makedirs(stem)
content = PdbStructure.get_pdb_content(result.pdb_code)
if content is None:
logger.debug("Encountered a problem downloading PDB %s - skipping entry", result.pdb_code)
else:
dat_content = simbad.db._str_to_dat(content)
with open(os.path.join(stem, result.pdb_code + ".dat"), "w") as f_out:
f_out.write(dat_content)
if simbad.db.is_valid_dat(os.path.join(stem, result.pdb_code + ".dat")):
pass
else:
logger.debug("Unable to convert %s to dat file", result.pdb_code)
if morda_installed_through_ccp4:
for dat_file in morda_dat_files:
if result.pdb_code.lower() == dat_file[0:4]:
stem = os.path.join(database, result.uniprot_mnemonic, result.uniprot_name, result.space_group,
"morda")
if not os.path.exists(stem):
os.makedirs(stem)
code = dat_file.rsplit('.', 1)[0]
final_file = os.path.join(stem, dat_file)
tmp_d = tmp_dir(directory=os.getcwd())
get_model_output = os.path.join(tmp_d, code + ".pdb")
cmd = [["export CCP4_SCR=", tmp_d], ["cd", tmp_d], [exe, "-c", code, "-m", "d"]]
script = Script(directory=tmp_d)
for c in cmd:
script.append(' '.join(map(str, c)))
collector.add(script)
log = script.path.rsplit('.', 1)[0] + '.log'
files += [(script.path, log, tmp_d, (get_model_output, final_file))]
if len(files) > 0:
scripts, _, tmps, files = zip(*files)
submit_chunk(collector=collector,
run_dir=os.getcwd(),
nproc=nproc,
job_name='cont_db',
submit_qtype=submit_qtype,
submit_queue=submit_queue,
permit_nonzero=True,
monitor=None,
success_func=None)
for output, final in files:
if os.path.isfile(output) and is_readable_file(output):
simbad.db.convert_pdb_to_dat(output, final)
else:
logger.critical("Problem with file: %s", output)
for d in tmps:
shutil.rmtree(d)
for f in dimple_files:
if os.path.isdir(f):
shutil.rmtree(f)
elif os.path.isfile(f):
os.remove(f)
validate_compressed_database(database)
def create_morda_db(database, nproc=2, submit_qtype=None, submit_queue=False, chunk_size=5000):
"""Create the MoRDa search database
Parameters
----------
database : str
The path to the database folder
nproc : int, optional
The number of processors [default: 2]
submit_qtype : str
The cluster submission queue type - currently support SGE and LSF
submit_queue : str
The queue to submit to on the cluster
chunk_size : int, optional
The number of jobs to submit at the same time [default: 5000]
Raises
------
RuntimeError
Windows is currently not supported
"""
if CUSTOM_PLATFORM == "windows":
msg = "Windows is currently not supported"
raise RuntimeError(msg)
if not is_valid_db_location(database):
raise RuntimeError("Permission denied! Cannot write to {}!".format(os.path.dirname(database)))
if "MRD_DB" in os.environ:
morda_installed_through_ccp4 = True
else:
download_morda()
morda_installed_through_ccp4 = False
morda_dat_path = os.path.join(os.environ['MRD_DB'], 'home', 'ca_DOM', '*.dat')
simbad_dat_path = os.path.join(database, '**', '*.dat')
morda_dat_files = set([os.path.basename(f) for f in glob.glob(morda_dat_path)])
simbad_dat_files = set([os.path.basename(f) for f in glob.glob(simbad_dat_path)])
erroneous_files = {"1bbzA_0.dat", "1gt0D_0.dat", "1h3oA_0.dat", "1kskA_1.dat", "1l0sA_0.dat"}
def delete_erroneous_files(erroneous_paths):
for f in erroneous_paths:
if os.path.isfile(f):
logger.warning("File flagged to be erroneous ... " + "removing from database: %s", f)
os.remove(f)
erroneous_paths = [os.path.join(database, name[1:3], name) for name in erroneous_files]
delete_erroneous_files(erroneous_paths)
dat_files = list(morda_dat_files - simbad_dat_files - erroneous_files)
if len(dat_files) < 1:
logger.info('SIMBAD database up-to-date')
if not morda_installed_through_ccp4:
shutil.rmtree(os.environ["MRD_DB"])
leave_timestamp(os.path.join(database, 'simbad_morda.txt'))
return
else:
logger.info("%d new entries were found in the MoRDa database, " + "updating SIMBAD database", len(dat_files))
exe = os.path.join(os.environ["MRD_PROG"], "get_model")
run_dir = tmp_dir(directory=os.getcwd())
# Submit in chunks, so we don't take too much disk space
# and can terminate without loosing the processed data
total_chunk_cycles = len(dat_files) // chunk_size + (len(dat_files) % 5 > 0)
for cycle, i in enumerate(range(0, len(dat_files), chunk_size)):
logger.info("Working on chunk %d out of %d", cycle + 1, total_chunk_cycles)
chunk_dat_files = dat_files[i:i + chunk_size]
# Create the database files
files = []
collector = ScriptCollector(None)
for f in chunk_dat_files:
code = os.path.basename(f).rsplit('.', 1)[0]
final_file = os.path.join(database, code[1:3], code + ".dat")
# We need a temporary directory within because "get_model" uses non-unique file names
tmp_d = tmp_dir(directory=run_dir)
get_model_output = os.path.join(tmp_d, code + ".pdb")
cmd = [["export CCP4_SCR=" + tmp_d],
["export MRD_DB=" + os.environ['MRD_DB']],
["cd", tmp_d],
[exe, "-c", code, "-m", "d"]]
script = Script(directory=tmp_d)
for c in cmd:
script.append(' '.join(map(str, c)))
collector.add(script)
log = script.path.rsplit('.', 1)[0] + '.log'
files += [(script.path, log, tmp_d, (get_model_output, final_file))]
scripts, _, tmps, files = zip(*files)
submit_chunk(collector=collector,
run_dir=os.getcwd(),
nproc=nproc,
job_name='morda_db',
submit_qtype=submit_qtype,
submit_queue=submit_queue,
permit_nonzero=True,
monitor=None,
success_func=None)
sub_dir_names = set([os.path.basename(f).rsplit('.', 1)[0][1:3] for f in chunk_dat_files])
for sub_dir_name in sub_dir_names:
sub_dir = os.path.join(database, sub_dir_name)
if os.path.isdir(sub_dir):
continue
os.makedirs(sub_dir)
for output, final in files:
if os.path.isfile(output) and is_readable_file(output):
simbad.db.convert_pdb_to_dat(output, final)
else:
logger.critical("Problem with file: %s", output)
for d in tmps:
shutil.rmtree(d)
shutil.rmtree(run_dir)
if not morda_installed_through_ccp4:
shutil.rmtree(os.environ["MRD_DB"])
validate_compressed_database(database)
leave_timestamp(os.path.join(database, 'simbad_morda.txt'))
def create_ensemble_db(database, pdb_db, nproc=2, submit_qtype=None, submit_queue=False, chunk_size=5000):
"""Create the MoRDa search database
Parameters
----------
database : str
The path to the database folder
pdb_db : str
The path to a local copy of the Protein Data Bank
nproc : int, optional
The number of processors [default: 2]
submit_qtype : str
The cluster submission queue type - currently support SGE and LSF
submit_queue : str
The queue to submit to on the cluster
chunk_size : int, optional
The number of jobs to submit at the same time [default: 5000]
Raises
------
RuntimeError
Windows is currently not supported
"""
if CUSTOM_PLATFORM == "windows":
msg = "Windows is currently not supported"
raise RuntimeError(msg)
if not is_valid_db_location(database):
raise RuntimeError("Permission denied! Cannot write to {}!".format(os.path.dirname(database)))
if "MRD_DB" in os.environ:
morda_installed_through_ccp4 = True
else:
download_morda()
morda_installed_through_ccp4 = False
morda_dat_path = os.path.join(os.environ['MRD_DB'], 'home', 'ca_DOM', '*.dat')
simbad_dat_path = os.path.join(database, '**', '*.dat')
morda_dat_files = set([os.path.basename(f) for f in glob.glob(morda_dat_path)])
simbad_dat_files = set([os.path.basename(f) for f in glob.glob(simbad_dat_path)])
erroneous_files = {"1bbzA_0.dat", "1gt0D_0.dat", "1h3oA_0.dat", "1kskA_1.dat", "1l0sA_0.dat"}
def delete_erroneous_files(erroneous_paths):
for f in erroneous_paths:
if os.path.isfile(f):
logger.warning("File flagged to be erroneous ... " + "removing from database: %s", f)
os.remove(f)
erroneous_paths = [os.path.join(database, name[1:3], name) for name in erroneous_files]
delete_erroneous_files(erroneous_paths)
dat_files = list(morda_dat_files - simbad_dat_files - erroneous_files)
if len(dat_files) < 1:
logger.info('SIMBAD ensemble database up-to-date')
if not morda_installed_through_ccp4:
shutil.rmtree(os.environ["MRD_DB"])
leave_timestamp(os.path.join(database, 'simbad_morda.txt'))
return
else:
logger.info("%d new entries were found in the MoRDa database, " + "updating SIMBAD ensemble database",
len(dat_files))
exe = os.path.join(os.environ["MRD_PROG"], "get_model")
mrbump_stdin = """
MDLS True
MDLC False
MDLD False
MDLP False
MDLM False
MDLU False
CHECK False
UPDATE False
PICKLE False
MRNUM 5
SCOP False
DEBUG False
RLEVEL 100
GESAMT_MERGE False
USEE True
GESE True
GEST True
AMPT False
DOPHMMER True
DOHHPRED False
PDBLOCAL {}
END
""".format(pdb_db)
run_dir = tmp_dir(directory=os.getcwd())
# Generate the sub directories in advance
sub_dir_names = set([os.path.basename(f).rsplit('.', 1)[0][1:3] for f in dat_files])
for sub_dir_name in sub_dir_names:
sub_dir = os.path.join(database, sub_dir_name)
if os.path.isdir(sub_dir):
continue
os.makedirs(sub_dir)
# Submit in chunks, so we don't take too much disk space
# and can terminate without loosing the processed data
total_chunk_cycles = len(dat_files) // chunk_size + (len(dat_files) % 5 > 0)
for cycle, i in enumerate(range(0, len(dat_files), chunk_size)):
logger.info("Working on chunk %d out of %d", cycle + 1, total_chunk_cycles)
chunk_dat_files = dat_files[i:i + chunk_size]
# Create the database files
files = []
collector = ScriptCollector(None)
for f in chunk_dat_files:
code = os.path.basename(f).rsplit('.', 1)[0]
final_file = os.path.join(database, code[1:3], code + ".dat")
# We need a temporary directory within because "get_model" uses non-unique file names
tmp_d = tmp_dir(directory=run_dir)
get_model_output = os.path.join(tmp_d, code + ".pdb")
get_seq_output = os.path.join(tmp_d, code + ".seq")
mrbump_directory = os.path.join(tmp_d, 'search_mrbump_1')
cmd = [["export CCP4_SCR=".format(tmp_d)],
["export MRD_DB=".format(os.environ['MRD_DB'])],
["cd", tmp_d],
[exe, "-c", code, "-m", "d"],
['ccp4-python', '-c', "'import simbad.util; "
"simbad.util.get_sequence(\"{0}\", \"{1}\")'".format(get_model_output,
get_seq_output)],
['mrbump', 'seqin', get_seq_output, '<< eof'],
[mrbump_stdin],
['eof'],
['ccp4-python', '-c', "'import simbad.util; "
"simbad.util.get_mrbump_ensemble(\"{0}\", \"{1}\")'".format(mrbump_directory,
final_file)]]
script = Script(directory=tmp_d)
for c in cmd:
script.append(' '.join(map(str, c)))
collector.add(script)
log = script.path.rsplit('.', 1)[0] + '.log'
files += [(script.path, log, tmp_d)]
scripts, _, tmps = zip(*files)
submit_chunk(collector=collector,
run_dir=os.getcwd(),
nproc=nproc,
job_name='ensemble_db',
submit_qtype=submit_qtype,
submit_queue=submit_queue,
permit_nonzero=True,
monitor=None,
success_func=None)
for d in tmps:
shutil.rmtree(d)
shutil.rmtree(run_dir)
if not morda_installed_through_ccp4:
shutil.rmtree(os.environ["MRD_DB"])
validate_compressed_database(database)
leave_timestamp(os.path.join(database, 'simbad_ensemble.txt'))
def create_db_custom(custom_db, database):
"""Create custom database
Parameters
----------
custom_db : str
The path to the input database of PDB files
database : str
The path to the output database folder
Raises
------
RuntimeError
Windows is currently not supported
"""
if CUSTOM_PLATFORM == "windows":
msg = "Windows is currently not supported"
raise RuntimeError(msg)
if not is_valid_db_location(custom_db):
raise RuntimeError("Permission denied! Cannot write to {}!".format(os.path.dirname(custom_db)))
custom_dat_files = set([
os.path.join(root, filename) for root, _, files in os.walk(custom_db) for filename in files
if filename.endswith('.pdb')
])
simbad_dat_path = os.path.join(database, '**', '*.dat')
simbad_dat_files = set([os.path.basename(f) for f in glob.glob(simbad_dat_path)])
dat_files = list(custom_dat_files - simbad_dat_files)
if len(dat_files) < 1:
logger.info('SIMBAD dat database up-to-date')
leave_timestamp(os.path.join(database, 'simbad_custom.txt'))
return
else:
logger.info("%d new entries were found in the custom database, updating SIMBAD database", len(dat_files))
files = []
for input_file in dat_files:
code = os.path.basename(input_file).rsplit('.', 1)[0]
time_stamp = str(datetime.datetime.now())
final_file = os.path.join(database, time_stamp, code + ".dat")
files += [(input_file, final_file)]
sub_dir = os.path.join(database, time_stamp)
if os.path.isdir(sub_dir):
continue
os.makedirs(sub_dir)
for output, final in files:
if os.path.isfile(output) and is_readable_file(output):
simbad.db.convert_pdb_to_dat(output, final)
else:
logger.critical("Problem with file: %s", output)
validate_compressed_database(database)
leave_timestamp(os.path.join(database, 'simbad_custom.txt'))
def create_db_argparse():
"""Argparse function database creationg"""
p = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
sp = p.add_subparsers(help='Database-specific commands')
pa = sp.add_parser('lattice', help='lattice database')
pa.set_defaults(which="lattice")
pa.add_argument(
'-debug_lvl',
type=str,
default='info',
help='The console verbosity level < notset | info | debug | warning | error | critical > ')
pa.add_argument('-latt_db', type=str, default=simbad.LATTICE_DB, help='Path to local copy of the lattice database')
pb = sp.add_parser('contaminant', help='Contaminant database')
pb.set_defaults(which="contaminant")
simbad.command_line._argparse_job_submission_options(pb)
pb.add_argument(
'-debug_lvl',
type=str,
default='info',
help='The console verbosity level < notset | info | debug | warning | error | critical > ')
pb.add_argument(
'-cont_db', type=str, default=simbad.CONTAMINANT_MODELS, help='Path to local copy of the contaminant database')
pb.add_argument(
'--add_morda_domains',
default=False,
action="store_true",
help="Retrospectively add morda domains to an updated contaminant database")
pc = sp.add_parser('morda', help='morda database')
pc.set_defaults(which="morda")
simbad.command_line._argparse_job_submission_options(pc)
pc.add_argument(
'-chunk_size', default=5000, type=int, help='Max jobs to submit at any given time [disk space dependent')
pc.add_argument(
'-debug_lvl',
type=str,
default='info',
help='The console verbosity level < notset | info | debug | warning | error | critical > ')
pc.add_argument('-simbad_db', type=str, default=simbad.MORDA_MODELS,
help='Path to local copy of the SIMBAD database')
pd = sp.add_parser('ensemble', help='ensemble database')
pd.set_defaults(which="ensemble")
simbad.command_line._argparse_job_submission_options(pd)
pd.add_argument(
'-chunk_size', default=5000, type=int, help='Max jobs to submit at any given time [disk space dependent')
pd.add_argument(
'-debug_lvl',
type=str,
default='info',
help='The console verbosity level < notset | info | debug | warning | error | critical > ')
pd.add_argument('-pdb_db', type=str, help="Path to a local copy of the Protein Data Bank")
pd.add_argument('ensemble_db', type=str, help='Path to local copy of the SIMBAD ensemble database')
pe = sp.add_parser('custom', help='custom database')
pe.set_defaults(which="custom")
pe.add_argument(
'custom_db', type=str, help='Path to local copy of the custom database of PDB files in SIMBAD format')
pe.add_argument(
'-debug_lvl',
type=str,
default='info',
help='The console verbosity level < notset | info | debug | warning | error | critical > ')
pe.add_argument('input_db', type=str, help='Path to local copy of the custom database of PDB files')
pf = sp.add_parser('validate', help='validate database')
pf.set_defaults(which="validate")
pf.add_argument(
'-debug_lvl',
type=str,
default='info',
help='The console verbosity level < notset | info | debug | warning | error | critical > ')
pf.add_argument('database', type=str, help='The database to validate')
return p
def leave_timestamp(f):
"""Write the current date & time to a file"""
with open(f, 'w') as f_out:
f_out.write(str(datetime.datetime.now()))
def validate_compressed_database(dir):
"""Validate an installation of a SIMBAD database"""
logger.info("Validating compressed database")
for directory, _, files in os.walk(dir):
for f in files:
infile = os.path.join(directory, f)
if infile.endswith(".dat"):
logger.debug("Validating file: %s", infile)
if not simbad.db.is_valid_dat(infile):
logger.critical("Corrupted file: %s", infile)
else:
logger.debug("Ignoring file: %s", infile)
def main():
"""SIMBAD database creation function"""
p = create_db_argparse()
args = p.parse_args()
global logger
logger = simbad.util.logging_util.setup_logging(args.debug_lvl)
simbad.command_line.print_header()
stopwatch = StopWatch()
stopwatch.start()
if args.which == "lattice":
create_lattice_db(args.latt_db)
elif args.which == "contaminant":
create_contaminant_db(
args.cont_db,
args.add_morda_domains,
nproc=args.nproc,
submit_qtype=args.submit_qtype,
submit_queue=args.submit_queue)
elif args.which == "morda":
create_morda_db(
args.simbad_db,
nproc=args.nproc,
submit_qtype=args.submit_qtype,
submit_queue=args.submit_queue,
chunk_size=args.chunk_size)
elif args.which == "ensemble":
create_ensemble_db(
args.ensemble_db,
pdb_db=args.pdb_db,
nproc=args.nproc,
submit_qtype=args.submit_qtype,
submit_queue=args.submit_queue,
chunk_size=args.chunk_size)
elif args.which == "custom":
create_db_custom(args.input_db, args.custom_db)
elif args.which == "validate":
if os.path.isdir(args.database):
validate_compressed_database(args.database)
else:
logger.critical("Unable to validate the following database: %s", args.database)
stopwatch.stop()
logger.info("Database creation completed in %d days, %d hours, %d minutes, and %d seconds", *stopwatch.time_pretty)
if os.path.exists('simbad.log'):
os.unlink('simbad.log')
if os.path.exists('debug.log'):
os.unlink('debug.log')
if __name__ == "__main__":
import logging
logging.basicConfig(level=logging.NOTSET)
try:
main()
except Exception:
simbad.exit.exit_error(*sys.exc_info())
|
rigdenlab/SIMBAD
|
simbad/command_line/simbad_database.py
|
Python
|
bsd-3-clause
| 33,539
|
[
"CRYSTAL"
] |
416da75f67d6b21d52e1616322fbcec9e8ee941f5b19a8ee06c5743c803a5079
|
# destiny_Wrapper/destiny_Wrapper.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called destiny_Wrapper
# User admin@galaxy.org at 19/08/2015 09:31:41
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#
# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# August 2014
# merged John Chilton's citation addition and ideas from Marius van den Beek to enable arbitrary
# data types for input and output - thanks!
#
# march 2014
# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
# grrrrr - night before a demo
# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
#
# added ghostscript and graphicsmagick as dependencies
# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
# errors ensued
#
# august 2013
# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
#
# july 2013
# added ability to combine images and individual log files into html output
# just make sure there's a log file foo.log and it will be output
# together with all images named like "foo_*.pdf
# otherwise old format for html
#
# January 2013
# problem pointed out by Carlos Borroto
# added escaping for <>$ - thought I did that ages ago...
#
# August 11 2012
# changed to use shell=False and cl as a sequence
# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
# It also serves as the wrapper for the new tool.
#
# you paste and run your script
# Only works for simple scripts that read one input from the history.
# Optionally can write one new history dataset,
# and optionally collect any number of outputs into links on an autogenerated HTML page.
# DO NOT install on a public or important site - please.
# installed generated tools are fine if the script is safe.
# They just run normally and their user cannot do anything unusually insecure
# but please, practice safe toolshed.
# Read the fucking code before you install any tool
# especially this one
# After you get the script working on some test data, you can
# optionally generate a toolshed compatible gzip file
# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
# safe and largely automated installation in a production Galaxy.
# If you opt for an HTML output, you get all the script outputs arranged
# as a single Html history item - all output files are linked, thumbnails for all the pdfs.
# Ugly but really inexpensive.
#
# Patches appreciated please.
#
#
# long route to June 2012 product
# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
# derived from an integrated script model
# called rgBaseScriptWrapper.py
# Note to the unwary:
# This tool allows arbitrary scripting on your Galaxy as the Galaxy user
# There is nothing stopping a malicious user doing whatever they choose
# Extremely dangerous!!
# Totally insecure. So, trusted users only
#
# preferred model is a developer using their throw away workstation instance - ie a private site.
# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
#
import sys
import shutil
import subprocess
import os
import time
import tempfile
import optparse
import tarfile
import re
import shutil
import math
progname = os.path.split(sys.argv[0])[1]
myversion = 'V001.1 March 2014'
verbose = False
debug = False
toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
reload(sys)
sys.setdefaultencoding('utf8')
# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
# tool xml
toolhtmldepskel = """<?xml version="1.0"?>
<tool_dependency>
<package name="ghostscript" version="9.10">
<repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
</package>
<package name="graphicsmagick" version="1.3.18">
<repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
</package>
<readme>
%s
</readme>
</tool_dependency>
"""
protorequirements = """<requirements>
<requirement type="package" version="9.10">ghostscript</requirement>
<requirement type="package" version="1.3.18">graphicsmagick</requirement>
</requirements>"""
def timenow():
"""return current time as a string
"""
return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
html_escape_table = {
"&": "&",
">": ">",
"<": "<",
"$": "\$"
}
def html_escape(text):
"""Produce entities within text."""
return "".join(html_escape_table.get(c,c) for c in text)
def cmd_exists(cmd):
return subprocess.call("type " + cmd, shell=True,
stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
def parse_citations(citations_text):
"""
"""
citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
citation_tuples = []
for citation in citations:
if citation.startswith("doi"):
citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
else:
citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
return citation_tuples
class ScriptRunner:
"""class is a wrapper for an arbitrary script
"""
def __init__(self,opts=None,treatbashSpecial=True):
"""
cleanup inputs, setup some outputs
"""
self.useGM = cmd_exists('gm')
self.useIM = cmd_exists('convert')
self.useGS = cmd_exists('gs')
self.temp_warned = False # we want only one warning if $TMP not set
self.treatbashSpecial = treatbashSpecial
if opts.output_dir: # simplify for the tool tarball
os.chdir(opts.output_dir)
self.thumbformat = 'png'
self.opts = opts
self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
self.toolid = self.toolname
self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
self.xmlfile = '%s.xml' % self.toolname
s = open(self.opts.script_path,'r').readlines()
s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
self.script = '\n'.join(s)
fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
tscript.write(self.script)
tscript.close()
self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
self.escapedScript = '\n'.join([html_escape(x) for x in s])
self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
if opts.output_dir: # may not want these complexities
self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
art = '%s.%s' % (self.toolname,opts.interpreter)
artpath = os.path.join(self.opts.output_dir,art) # need full path
artifact = open(artpath,'w') # use self.sfile as script source for Popen
artifact.write(self.script)
artifact.close()
self.cl = []
self.html = []
a = self.cl.append
a(opts.interpreter)
if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
a(self.sfile)
else:
a('-') # stdin
a(opts.input_tab)
a(opts.input_int)
a(opts.input_sigma)
a(opts.plot_pergene)
a(opts.input_gene)
a(opts.output_tab)
a(opts.output_tab2)
self.outputFormat = self.opts.output_format
self.inputFormats = self.opts.input_formats
self.test1Input = '%s_test1_input.xls' % self.toolname
self.test1Output = '%s_test1_output.xls' % self.toolname
self.test1HTML = '%s_test1_output.html' % self.toolname
def makeXML(self):
"""
Create a Galaxy xml tool wrapper for the new script as a string to write out
fixme - use templating or something less fugly than this example of what we produce
<tool id="reverse" name="reverse" version="0.01">
<description>a tabular file</description>
<command interpreter="python">
reverse.py --script_path "$runMe" --interpreter "python"
--tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
</command>
<inputs>
<param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
</inputs>
<outputs>
<data format="tabular" name="tab_file" label="${job_name}"/>
</outputs>
<help>
**What it Does**
Reverse the columns in a tabular file
</help>
<configfiles>
<configfile name="runMe">
# reverse order of columns in a tabular file
import sys
inp = sys.argv[1]
outp = sys.argv[2]
i = open(inp,'r')
o = open(outp,'w')
for row in i:
rs = row.rstrip().split('\t')
rs.reverse()
o.write('\t'.join(rs))
o.write('\n')
i.close()
o.close()
</configfile>
</configfiles>
</tool>
"""
newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
%(tooldesc)s
%(requirements)s
<command interpreter="python">
%(command)s
</command>
<inputs>
%(inputs)s
</inputs>
<outputs>
%(outputs)s
</outputs>
<configfiles>
<configfile name="runMe">
%(script)s
</configfile>
</configfiles>
%(tooltests)s
<help>
%(help)s
</help>
<citations>
%(citations)s
<citation type="doi">10.1093/bioinformatics/bts573</citation>
</citations>
</tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
newCommand="""
%(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
--tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
# may NOT be an input or htmlout - appended later
tooltestsTabOnly = """
<tests>
<test>
<param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
<param name="job_name" value="test1"/>
<param name="runMe" value="$runMe"/>
<output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s"/>
</test>
</tests>
"""
tooltestsHTMLOnly = """
<tests>
<test>
<param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
<param name="job_name" value="test1"/>
<param name="runMe" value="$runMe"/>
<output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
</test>
</tests>
"""
tooltestsBoth = """<tests>
<test>
<param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
<param name="job_name" value="test1"/>
<param name="runMe" value="$runMe"/>
<output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s" />
<output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
</test>
</tests>
"""
xdict = {}
xdict['outputFormat'] = self.outputFormat
xdict['inputFormats'] = self.inputFormats
xdict['requirements'] = ''
if self.opts.make_HTML:
if self.opts.include_dependencies == "yes":
xdict['requirements'] = protorequirements
xdict['tool_version'] = self.opts.tool_version
xdict['test1Input'] = self.test1Input
xdict['test1HTML'] = self.test1HTML
xdict['test1Output'] = self.test1Output
if self.opts.make_HTML and self.opts.output_tab <> 'None':
xdict['tooltests'] = tooltestsBoth % xdict
elif self.opts.make_HTML:
xdict['tooltests'] = tooltestsHTMLOnly % xdict
else:
xdict['tooltests'] = tooltestsTabOnly % xdict
xdict['script'] = self.escapedScript
# configfile is least painful way to embed script to avoid external dependencies
# but requires escaping of <, > and $ to avoid Mako parsing
if self.opts.help_text:
helptext = open(self.opts.help_text,'r').readlines()
helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
xdict['help'] = ''.join([x for x in helptext])
else:
xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
if self.opts.citations:
citationstext = open(self.opts.citations,'r').read()
citation_tuples = parse_citations(citationstext)
citations_xml = ""
for citation_type, citation_content in citation_tuples:
citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
citations_xml += citation_xml
xdict['citations'] = citations_xml
else:
xdict['citations'] = ""
coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
coda.append('\n')
coda.append(self.indentedScript)
coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
coda.append('See %s for details of that project' % (toolFactoryURL))
coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
if self.opts.tool_desc:
xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
else:
xdict['tooldesc'] = ''
xdict['command_outputs'] = ''
xdict['outputs'] = ''
if self.opts.input_tab <> 'None':
xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
else:
xdict['command_inputs'] = '' # assume no input - eg a random data generator
xdict['inputs'] = ''
xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
xdict['toolname'] = self.toolname
xdict['toolid'] = self.toolid
xdict['interpreter'] = self.opts.interpreter
xdict['scriptname'] = self.sfile
if self.opts.make_HTML:
xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
else:
xdict['command_outputs'] += ' --output_dir "./"'
if self.opts.output_tab <> 'None':
xdict['command_outputs'] += ' --output_tab "$tab_file"'
xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outputFormat
xdict['command'] = newCommand % xdict
xmls = newXML % xdict
xf = open(self.xmlfile,'w')
xf.write(xmls)
xf.write('\n')
xf.close()
# ready for the tarball
def makeTooltar(self):
"""
a tool is a gz tarball with eg
/toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
"""
retval = self.run()
if retval:
print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
sys.exit(1)
tdir = self.toolname
os.mkdir(tdir)
self.makeXML()
if self.opts.make_HTML:
if self.opts.help_text:
hlp = open(self.opts.help_text,'r').read()
else:
hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
if self.opts.include_dependencies:
tooldepcontent = toolhtmldepskel % hlp
depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
depf.write(tooldepcontent)
depf.write('\n')
depf.close()
if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
testdir = os.path.join(tdir,'test-data')
os.mkdir(testdir) # make tests directory
shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
if self.opts.output_tab <> 'None':
shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
if self.opts.make_HTML:
shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
if self.opts.output_dir:
shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
outpif = '%s.py' % self.toolname # new name
outpiname = os.path.join(tdir,outpif) # path for the tool tarball
pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
notes += pi
outpi = open(outpiname,'w')
outpi.write(''.join(notes))
outpi.write('\n')
outpi.close()
stname = os.path.join(tdir,self.sfile)
if not os.path.exists(stname):
shutil.copyfile(self.sfile, stname)
xtname = os.path.join(tdir,self.xmlfile)
if not os.path.exists(xtname):
shutil.copyfile(self.xmlfile,xtname)
tarpath = "%s.gz" % self.toolname
tar = tarfile.open(tarpath, "w:gz")
tar.add(tdir,arcname=self.toolname)
tar.close()
shutil.copyfile(tarpath,self.opts.new_tool)
shutil.rmtree(tdir)
## TODO: replace with optional direct upload to local toolshed?
return retval
def compressPDF(self,inpdf=None,thumbformat='png'):
"""need absolute path to pdf
note that GS gets confoozled if no $TMP or $TEMP
so we set it
"""
assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
sto = open(hlog,'a')
our_env = os.environ.copy()
our_tmp = our_env.get('TMP',None)
if not our_tmp:
our_tmp = our_env.get('TEMP',None)
if not (our_tmp and os.path.exists(our_tmp)):
newtmp = os.path.join(self.opts.output_dir,'tmp')
try:
os.mkdir(newtmp)
except:
sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
our_env['TEMP'] = newtmp
if not self.temp_warned:
sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
self.temp_warned = True
outpdf = '%s_compressed' % inpdf
cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
retval1 = x.wait()
sto.close()
if retval1 == 0:
os.unlink(inpdf)
shutil.move(outpdf,inpdf)
os.unlink(hlog)
hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
sto = open(hlog,'w')
outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
if self.useGM:
cl2 = ['gm', 'convert', inpdf, outpng]
else: # assume imagemagick
cl2 = ['convert', inpdf + '[0]', outpng]
x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
retval2 = x.wait()
sto.close()
if retval2 == 0:
os.unlink(hlog)
retval = retval1 or retval2
return retval
def getfSize(self,fpath,outpath):
"""
format a nice file size string
"""
size = ''
fp = os.path.join(outpath,fpath)
if os.path.isfile(fp):
size = '0 B'
n = float(os.path.getsize(fp))
if n > 2**20:
size = '%1.1f MB' % (n/2**20)
elif n > 2**10:
size = '%1.1f KB' % (n/2**10)
elif n > 0:
size = '%d B' % (int(n))
return size
def makeHtml(self):
""" Create an HTML file content to list all the artifacts found in the output_dir
"""
galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
<title></title>
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
</head>
<body>
<div class="toolFormBody">
"""
galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
galhtmlpostfix = """</div></body></html>\n"""
flist = os.listdir(self.opts.output_dir)
flist = [x for x in flist if x <> 'Rplots.pdf']
flist.sort()
html = []
html.append(galhtmlprefix % progname)
html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
fhtml = []
if len(flist) > 0:
logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
logfiles.sort()
logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
logfiles.append(os.path.abspath(self.tlog)) # make it the last one
pdflist = []
npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf' or os.path.splitext(x)[-1].lower() == '.png'])
for rownum,fname in enumerate(flist):
dname,e = os.path.splitext(fname)
sfsize = self.getfSize(fname,self.opts.output_dir)
if e.lower() == '.pdf' or e.lower() == '.png': # compress and make a thumbnail
thumb = '%s.%s' % (dname,self.thumbformat)
pdff = os.path.join(self.opts.output_dir,fname)
retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
if retval == 0:
pdflist.append((fname,thumb))
else:
pdflist.append((fname,fname))
if (rownum+1) % 2 == 0:
fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
else:
fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
for logfname in logfiles: # expect at least tlog - if more
if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
sectionname = 'All tool run'
if (len(logfiles) > 1):
sectionname = 'Other'
ourpdfs = pdflist
else:
realname = os.path.basename(logfname)
sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
nacross = 1
npdf = len(ourpdfs)
if npdf > 0:
nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
if int(nacross)**2 != npdf:
nacross += 1
nacross = int(nacross)
width = min(400,int(1200/nacross))
html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
ntogo = nacross # counter for table row padding with empty cells
html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
for i,paths in enumerate(ourpdfs):
fname,thumb = paths
s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
if ((i+1) % nacross == 0):
s += '</tr>\n'
ntogo = 0
if i < (npdf - 1): # more to come
s += '<tr>'
ntogo = nacross
else:
ntogo -= 1
html.append(s)
if html[-1].strip().endswith('</tr>'):
html.append('</table></div>\n')
else:
if ntogo > 0: # pad
html.append('<td> </td>'*ntogo)
html.append('</tr></table></div>\n')
#logt = open(logfname,'r').readlines()
#logtext = [x for x in logt if x.strip() > '']
#html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
#if len(logtext) > 1:
# html.append('\n<pre>\n')
# html += logtext
# html.append('\n</pre>\n')
#else:
# html.append('%s is empty<br/>' % logfname)
if len(fhtml) > 0:
fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
fhtml.append('</table></div><br/>')
html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
html += fhtml # add all non-pdf files to the end of the display
else:
html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
html.append(galhtmlpostfix)
htmlf = file(self.opts.output_html,'w')
htmlf.write('\n'.join(html))
htmlf.write('\n')
htmlf.close()
self.html = html
def run(self):
"""
scripts must be small enough not to fill the pipe!
"""
if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
retval = self.runBash()
else:
if self.opts.output_dir:
ste = open(self.elog,'w')
sto = open(self.tlog,'w')
sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
sto.flush()
p = subprocess.Popen(self.cl,shell=False,stdout=subprocess.PIPE,stderr=subprocess.PIPE,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
#p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
else:
p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
p.stdin.write(self.script)
#p.stdin.close()
stdout_data, stderr_data = p.communicate()
p.stdin.close()
#retval = p.wait()
retval = p.returncode
if self.opts.output_dir:
sto.close()
ste.close()
err = stderr_data
#err = open(self.elog,'r').readlines()
print >> sys.stdout, stdout_data
if retval <> 0 and err: # problem
print >> sys.stderr,err.encode('raw_unicode_escape').decode('ascii')
if self.opts.make_HTML:
self.makeHtml()
return retval
def runBash(self):
"""
cannot use - for bash so use self.sfile
"""
if self.opts.output_dir:
s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
sto = open(self.tlog,'w')
sto.write(s)
sto.flush()
p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
else:
p = subprocess.Popen(self.cl,shell=False)
retval = p.wait()
if self.opts.output_dir:
sto.close()
if self.opts.make_HTML:
self.makeHtml()
return retval
def main():
u = """
This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
<command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
</command>
"""
op = optparse.OptionParser()
a = op.add_option
a('--script_path',default=None)
a('--tool_name',default=None)
a('--interpreter',default=None)
a('--output_dir',default='./')
a('--output_html',default=None)
a('--input_tab',default="None")
a('--input_int',default="None")
a('--input_sigma',default="None")
a('--plot_pergene',default="None")
a('--input_gene',default="None")
a('--input_formats',default="tabular,text")
a('--output_tab',default="None")
a('--output_tab2',default="None")
a('--output_format',default="tabular")
a('--user_email',default='Unknown')
a('--bad_user',default=None)
a('--make_Tool',default=None)
a('--make_HTML',default=None)
a('--help_text',default=None)
a('--citations',default=None)
a('--tool_desc',default=None)
a('--new_tool',default=None)
a('--tool_version',default=None)
a('--include_dependencies',default=None)
opts, args = op.parse_args()
assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
if opts.output_dir:
try:
os.makedirs(opts.output_dir)
except:
pass
r = ScriptRunner(opts)
if opts.make_Tool:
retcode = r.makeTooltar()
else:
retcode = r.run()
os.unlink(r.sfile)
if retcode:
sys.exit(retcode) # indicate failure to job runner
if __name__ == "__main__":
main()
|
myoshimura080822/tools_of_rnaseq_on_docker_galaxy
|
destiny_Wrapper/destiny_Wrapper.py
|
Python
|
mit
| 32,902
|
[
"Galaxy"
] |
8c83fede97b77c718e38977ae520031e57dfab8ca3648fbc37dda49e159f4e81
|
import copy
# flake8: noqa
LSPCI = """
0000:00:00.0 "Host bridge" "Intel Corporation" "Haswell-E DMI2" -r02 "Intel Corporation" "Device 0000"
0000:00:03.0 "PCI bridge" "Intel Corporation" "Haswell-E PCI Express Root Port 3" -r02 "" ""
0000:00:03.2 "PCI bridge" "Intel Corporation" "Haswell-E PCI Express Root Port 3" -r02 "" ""
0000:00:05.0 "System peripheral" "Intel Corporation" "Haswell-E Address Map, VTd_Misc, System Management" -r02 "" ""
0000:00:05.1 "System peripheral" "Intel Corporation" "Haswell-E Hot Plug" -r02 "" ""
0000:00:05.2 "System peripheral" "Intel Corporation" "Haswell-E RAS, Control Status and Global Errors" -r02 "" ""
0000:00:05.4 "PIC" "Intel Corporation" "Haswell-E I/O Apic" -r02 -p20 "Intel Corporation" "Device 0000"
0000:00:11.0 "Unassigned class [ff00]" "Intel Corporation" "Wellsburg SPSR" -r05 "Intel Corporation" "Device 7270"
0000:00:11.4 "SATA controller" "Intel Corporation" "Wellsburg sSATA Controller [AHCI mode]" -r05 -p01 "Cisco Systems Inc" "Device 0067"
0000:00:16.0 "Communication controller" "Intel Corporation" "Wellsburg MEI Controller #1" -r05 "Intel Corporation" "Device 7270"
0000:00:16.1 "Communication controller" "Intel Corporation" "Wellsburg MEI Controller #2" -r05 "Intel Corporation" "Device 7270"
0000:00:1a.0 "USB controller" "Intel Corporation" "Wellsburg USB Enhanced Host Controller #2" -r05 -p20 "Intel Corporation" "Device 7270"
0000:00:1c.0 "PCI bridge" "Intel Corporation" "Wellsburg PCI Express Root Port #1" -rd5 "" ""
0000:00:1c.3 "PCI bridge" "Intel Corporation" "Wellsburg PCI Express Root Port #4" -rd5 "" ""
0000:00:1c.4 "PCI bridge" "Intel Corporation" "Wellsburg PCI Express Root Port #5" -rd5 "" ""
0000:00:1d.0 "USB controller" "Intel Corporation" "Wellsburg USB Enhanced Host Controller #1" -r05 -p20 "Intel Corporation" "Device 7270"
0000:00:1f.0 "ISA bridge" "Intel Corporation" "Wellsburg LPC Controller" -r05 "Intel Corporation" "Device 7270"
0000:00:1f.2 "SATA controller" "Intel Corporation" "Wellsburg 6-Port SATA Controller [AHCI mode]" -r05 -p01 "Cisco Systems Inc" "Device 0067"
0000:01:00.0 "PCI bridge" "Cisco Systems Inc" "VIC 82 PCIe Upstream Port" -r01 "" ""
0000:02:00.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Downstream Port" -ra2 "" ""
0000:02:01.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Downstream Port" -ra2 "" ""
0000:03:00.0 "Unclassified device [00ff]" "Cisco Systems Inc" "VIC Management Controller" -ra2 "Cisco Systems Inc" "Device 012e"
0000:04:00.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Upstream Port" -ra2 "" ""
0000:05:00.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Downstream Port" -ra2 "" ""
0000:05:01.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Downstream Port" -ra2 "" ""
0000:05:02.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Downstream Port" -ra2 "" ""
0000:05:03.0 "PCI bridge" "Cisco Systems Inc" "VIC PCIe Downstream Port" -ra2 "" ""
0000:06:00.0 "Ethernet controller" "Cisco Systems Inc" "VIC Ethernet NIC" -ra2 "Cisco Systems Inc" "Device 012e"
0000:07:00.0 "Ethernet controller" "Cisco Systems Inc" "VIC Ethernet NIC" -ra2 "Cisco Systems Inc" "Device 012e"
0000:08:00.0 "Fibre Channel" "Cisco Systems Inc" "VIC FCoE HBA" -ra2 "Cisco Systems Inc" "Device 012e"
0000:09:00.0 "Fibre Channel" "Cisco Systems Inc" "VIC FCoE HBA" -ra2 "Cisco Systems Inc" "Device 012e"
0000:0b:00.0 "RAID bus controller" "LSI Logic / Symbios Logic" "MegaRAID SAS-3 3108 [Invader]" -r02 "Cisco Systems Inc" "Device 00db"
0000:0f:00.0 "VGA compatible controller" "Matrox Electronics Systems Ltd." "MGA G200e [Pilot] ServerEngines (SEP1)" -r02 "Cisco Systems Inc" "Device 0101"
0000:10:00.0 "Ethernet controller" "Intel Corporation" "I350 Gigabit Network Connection" -r01 "Cisco Systems Inc" "Device 00d6"
0000:10:00.1 "Ethernet controller" "Intel Corporation" "I350 Gigabit Network Connection" -r01 "Cisco Systems Inc" "Device 00d6"
0000:7f:08.0 "System peripheral" "Intel Corporation" "Haswell-E QPI Link 0" -r02 "Intel Corporation" "Haswell-E QPI Link 0"
"""
CONFD_CLI = """
NAME PHYS ADDRESS
--------------------------------------------
TenGigabitEthernet6/0/0 84:b8:02:2a:5f:c3
TenGigabitEthernet7/0/0 84:b8:02:2a:5f:c4
local0 -
"""
CONFD_CLI_ONE_MISSING = """
NAME PHYS ADDRESS
--------------------------------------------
TenGigabitEthernet6/0/0 84:b8:02:2a:5f:c3
local0 -
"""
CONFD_CLI_INVMAC = """
NAME PHYS ADDRESS
--------------------------------------------
TenGigabitEthernet6/0/0 no:ta:va:li:dm:ac
TenGigabitEthernet7/0/0 84:b8:02:2a:5f:c4
local0 -
"""
CONFD_CLI_NODEVS = """
NAME PHYS ADDRESS
--------------------------------------------
local0 -
"""
CONFD_CLI_NOLOCAL = """
NAME PHYS ADDRESS
--------------------------------------------
"""
SYS_TREE = {
'/sys/class/net/eth2': '../../devices/pci0000:00/0000:00:1c.4/0000:10:00.0/net/eth2',
'/sys/class/net/eth3': '../../devices/pci0000:00/0000:00:1c.4/0000:10:00.1/net/eth3',
'/sys/class/net/juju-br0': '../../devices/virtual/net/juju-br0',
'/sys/class/net/lo': '../../devices/virtual/net/lo',
'/sys/class/net/lxcbr0': '../../devices/virtual/net/lxcbr0',
'/sys/class/net/veth1GVRCF': '../../devices/virtual/net/veth1GVRCF',
'/sys/class/net/veth7AXEUK': '../../devices/virtual/net/veth7AXEUK',
'/sys/class/net/vethACOIJJ': '../../devices/virtual/net/vethACOIJJ',
'/sys/class/net/vethMQ819H': '../../devices/virtual/net/vethMQ819H',
'/sys/class/net/virbr0': '../../devices/virtual/net/virbr0',
'/sys/class/net/virbr0-nic': '../../devices/virtual/net/virbr0-nic',
'/sys/devices/pci0000:00/0000:00:1c.4/0000:10:00.0/net/eth2/device': '../../../0000:10:00.0',
'/sys/devices/pci0000:00/0000:00:1c.4/0000:10:00.1/net/eth3/device': '../../../0000:10:00.1',
}
LSPCI_KS_IGB_UNBOUND = """
{} Ethernet controller: Intel Corporation I350 Gigabit Network Connection (rev 01)
Subsystem: Cisco Systems Inc Device 00d6
"""
LSPCI_KS_IGB_BOUND = """
{} Ethernet controller: Intel Corporation I350 Gigabit Network Connection (rev 01)
Subsystem: Cisco Systems Inc Device 00d6
Kernel driver in use: igb
"""
LSPCI_KS_IGBUIO_BOUND = """
{} Ethernet controller: Cisco Systems Inc VIC Ethernet NIC (rev a2)
Subsystem: Cisco Systems Inc VIC 1240 MLOM Ethernet NIC
Kernel driver in use: igb_uio
"""
LSPCI_KS = {
'0000:06:00.0': LSPCI_KS_IGBUIO_BOUND.format('06:00.0'),
'0000:10:00.0': LSPCI_KS_IGB_BOUND.format('10:00.0'),
}
MODALIAS = """
alias pci:v00001137d00000071sv*sd*bc*sc*i* enic
alias pci:v00001137d00000044sv*sd*bc*sc*i* enic
alias pci:v00001137d00000043sv*sd*bc*sc*i* enic
alias pci:v00008086d000010D6sv*sd*bc*sc*i* igb
alias pci:v00008086d000010A9sv*sd*bc*sc*i* igb
alias pci:v00008086d00001522sv*sd*bc*sc*i* igb
alias pci:v00008086d00001521sv*sd*bc*sc*i* igb
alias pci:v00008086d0000157Csv*sd*bc*sc*i* igb
"""
LSPCI_NS = {
'0000:06:00.0': "06:00.0 0200: 1137:0043 (rev a2)",
'0000:07:00.0': "07:00.0 0200: 1137:0043 (rev a2)",
'0000:10:00.0': "10:00.0 0200: 8086:1521 (rev 01)",
'0000:10:00.1': "10:00.1 0200: 8086:1521 (rev 01)",
}
FILE_CONTENTS = {
'/sys/class/net/eth2/address': 'a8:9d:21:cf:93:fc',
'/sys/class/net/eth3/address': 'a8:9d:21:cf:93:fd',
'/sys/class/net/eth2/operstate': 'up',
'/sys/class/net/eth3/operstate': 'down',
'/lib/modules/3.13.0-35-generic/modules.alias': MODALIAS,
}
COMMANDS = {
'LSPCI_MD': ['lspci', '-m', '-D'],
'LSPCI_KS': ['lspci', '-ks'],
'LSPCI_NS': ['lspci', '-ns'],
'UNAME_R': ['uname', '-r'],
'CONFD_CLI': ['/opt/cisco/vpe/bin/confd_cli', '-N', '-C', '-u', 'system'],
}
NET_SETUP = {
'LSPCI_MD': LSPCI,
'UNAME_R': '3.13.0-35-generic',
'CONFD_CLI': CONFD_CLI,
'0000:06:00.0': {
'LSPCI_KS': LSPCI_KS_IGBUIO_BOUND.format('06:00.0'),
'LSPCI_NS': "06:00.0 0200: 1137:0043 (rev a2)",
},
'0000:07:00.0': {
'LSPCI_KS': LSPCI_KS_IGBUIO_BOUND.format('07:00.0'),
'LSPCI_NS': "07:00.0 0200: 1137:0043 (rev a2)",
},
'0000:10:00.0': {
'LSPCI_KS': LSPCI_KS_IGB_BOUND.format('10:00.0'),
'LSPCI_NS': "10:00.0 0200: 8086:1521 (rev 01)",
},
'0000:10:00.1': {
'LSPCI_KS': LSPCI_KS_IGB_BOUND.format('10:00.1'),
'LSPCI_NS': "10:00.1 0200: 8086:1521 (rev 01)",
},
}
NET_SETUP_ORPHAN = copy.deepcopy(NET_SETUP)
NET_SETUP_ORPHAN['CONFD_CLI'] = CONFD_CLI_ONE_MISSING
NET_SETUP_ORPHAN['0000:07:00.0']['LSPCI_KS'] = LSPCI_KS_IGB_UNBOUND.format('07:00.0')
QN_CONF = """
lc_procs = { svm_cleanup vpe confd orca }
install_root = "/cisco"
svm_cleanup = {
pgm = "$(install_root)/bin/svm_cleanup",
run_once = "yes",
max_synchronous_wait = "5.0",
console_output = "yes"
}
vpe = {
pgm = "$(install_root)/bin/vpe",
args = "unix { nodaemon log /tmp/vpe.log cli-listen localhost:5002 full-coredump } api-trace { on } dpdk { socket-mem 1024 dev 0000:00:06.0 }",
max_cpu_percent = "111.0",
console_output = "yes",
crash_reset_all="yes"
}
confd = {
pgm = "$(install_root)/bin/confd",
args = "--foreground -c $(install_root)/etc/confd/confd.conf",
max_cpu_percent = "111.0",
crash_reset_all="yes"
}
orca = {
pgm = "$(install_root)/bin/orca",
args = "unix { nodaemon log /tmp/orca.log cli-listen localhost:5003 }",
console_output = "yes",
max_cpu_percent = "111.0",
crash_reset_all="yes"
"""
DPKG_L = """
ii net-tools 1.60-25ubuntu2.1 amd64 The NET-3 networking toolkit
ii netbase 5.2 all Basic TCP/IP networking system
ii netcat-openbsd 1.105-7ubuntu1 amd64 TCP/IP swiss army knife
ii nova-common 1:2014.1.4-0ubuntu2.1.1~ppa201506221720 all OpenStack Compute - common files
"""
|
coreycb/charms.openstack
|
unit_tests/pci_responses.py
|
Python
|
apache-2.0
| 10,045
|
[
"ORCA"
] |
d7419981a29e65332417c38b7b07479af47b337987e912401b6ad260ef75c36a
|
import sys
from mpi4py import MPI
import numpy as np
from delight.io import *
from delight.utils import *
from delight.photoz_gp import PhotozGP
from delight.photoz_kernels import Photoz_mean_function, Photoz_kernel
from delight.utils_cy import approx_flux_likelihood_cy
# Parse parameters file
if len(sys.argv) < 2:
raise Exception('Please provide a parameter file')
params = parseParamFile(sys.argv[1], verbose=False)
# Read filter coefficients, compute normalization of filters
bandCoefAmplitudes, bandCoefPositions, bandCoefWidths, norms\
= readBandCoefficients(params)
numBands = bandCoefAmplitudes.shape[0]
redshiftDistGrid, redshiftGrid, redshiftGridGP = createGrids(params)
f_mod = readSEDs(params)
DL = approx_DL()
dir_seds = params['templates_directory']
dir_filters = params['bands_directory']
lambdaRef = params['lambdaRef']
sed_names = params['templates_names']
f_mod_grid = np.zeros((redshiftGrid.size, len(sed_names),
len(params['bandNames'])))
for t, sed_name in enumerate(sed_names):
f_mod_grid[:, t, :] = np.loadtxt(dir_seds + '/' + sed_name +
'_fluxredshiftmod.txt')
numZbins = redshiftDistGrid.size - 1
numZ = redshiftGrid.size
numConfLevels = len(params['confidenceLevels'])
numObjectsTraining = np.sum(1 for line in open(params['training_catFile']))
numObjectsTarget = np.sum(1 for line in open(params['target_catFile']))
print('Number of Training Objects', numObjectsTraining)
print('Number of Target Objects', numObjectsTarget)
for ellPriorSigma in [1.0, 10.0]:
alpha_C = 1e3
alpha_L = 1e2
V_C, V_L = 1.0, 1.0
gp = PhotozGP(
f_mod,
bandCoefAmplitudes, bandCoefPositions, bandCoefWidths,
params['lines_pos'], params['lines_width'],
V_C, V_L, alpha_C, alpha_L,
redshiftGridGP, use_interpolators=True)
for extraFracFluxError in [1e-2]:
redshifts = np.zeros((numObjectsTraining, ))
bestTypes = np.zeros((numObjectsTraining, ), dtype=int)
ellMLs = np.zeros((numObjectsTraining, ))
model_mean = np.zeros((numZ, numObjectsTraining, numBands))
model_covar = np.zeros((numZ, numObjectsTraining, numBands))
# params['training_extraFracFluxError'] = extraFracFluxError
params['target_extraFracFluxError'] = extraFracFluxError
for V_C in [0.1, 1.0]:
gp.var_C = V_C
gp.var_L = V_L
loc = - 1
trainingDataIter = getDataFromFile(
params, 0, numObjectsTraining,
prefix="training_", getXY=True)
for z, normedRefFlux, bands, fluxes,\
fluxesVar, bCV, fCV, fvCV, X, Y, Yvar\
in trainingDataIter:
loc += 1
redshifts[loc] = z
themod = np.zeros((1, f_mod_grid.shape[1], bands.size))
for it in range(f_mod_grid.shape[1]):
for ib, band in enumerate(bands):
themod[0, it, ib] = np.interp(z, redshiftGrid,
f_mod_grid[:, it, band])
chi2_grid, theellMLs = scalefree_flux_likelihood(
fluxes,
fluxesVar,
themod,
returnChi2=True
)
bestTypes[loc] = np.argmin(chi2_grid)
ellMLs[loc] = theellMLs[0, bestTypes[loc]]
X[:, 2] = ellMLs[loc]
gp.setData(X, Y, Yvar, bestTypes[loc])
model_mean[:, loc, :], model_covar[:, loc, :] =\
gp.predictAndInterpolate(redshiftGrid, ell=ellMLs[loc])
for redshiftSigma in [0.1, 1.0]:
loc = - 1
targetDataIter = getDataFromFile(params, 0, numObjectsTarget,
prefix="target_", getXY=False)
bias_zmap = np.zeros((redshiftDistGrid.size, ))
bias_zmean = np.zeros((redshiftDistGrid.size, ))
confFractions = np.zeros((numConfLevels,
redshiftDistGrid.size))
binnobj = np.zeros((redshiftDistGrid.size, ))
bias_nz = np.zeros((redshiftDistGrid.size, ))
stackedPdfs = np.zeros((redshiftGrid.size,
redshiftDistGrid.size))
cis = np.zeros((numObjectsTarget, ))
zmeanBinLocs = np.zeros((numObjectsTarget, ), dtype=int)
for z, normedRefFlux, bands, fluxes, fluxesVar, bCV, fCV, fvCV\
in targetDataIter:
loc += 1
like_grid = np.zeros((model_mean.shape[0],
model_mean.shape[1]))
ell_hat_z = normedRefFlux * 4 * np.pi\
* params['fluxLuminosityNorm'] \
* (DL(redshiftGrid)**2. * (1+redshiftGrid))
ell_hat_z[:] = 1
approx_flux_likelihood_cy(
like_grid,
model_mean.shape[0], model_mean.shape[1], bands.size,
fluxes, fluxesVar,
model_mean[:, :, bands],
V_C*model_covar[:, :, bands],
ell_hat_z, (ell_hat_z*ellPriorSigma)**2)
like_grid *= np.exp(-0.5*((redshiftGrid[:, None] -
redshifts[None, :]) /
redshiftSigma)**2)
pdf = like_grid.sum(axis=1)
if pdf.sum() == 0:
print("NULL PDF with galaxy", loc)
if pdf.sum() > 0:
metrics\
= computeMetrics(z, redshiftGrid, pdf,
params['confidenceLevels'])
ztrue, zmean, zstdzmean, zmap, zstdzmean,\
pdfAtZ, cumPdfAtZ = metrics[0:7]
confidencelevels = metrics[7:]
zmeanBinLoc = -1
for i in range(numZbins):
if zmean >= redshiftDistGrid[i]\
and zmean < redshiftDistGrid[i+1]:
zmeanBinLoc = i
bias_zmap[i] += ztrue - zmap
bias_zmean[i] += ztrue - zmean
binnobj[i] += 1
bias_nz[i] += ztrue
zmeanBinLocs[loc] = zmeanBinLoc
for i in range(numConfLevels):
if pdfAtZ >= confidencelevels[i]:
confFractions[i, zmeanBinLoc] += 1
stackedPdfs[:, zmeanBinLoc]\
+= pdf / numObjectsTraining
ind = pdf >= pdfAtZ
pdf /= np.trapz(pdf, x=redshiftGrid)
cis[loc] = np.trapz(pdf[ind], x=redshiftGrid[ind])
confFractions /= binnobj[None, :]
bias_nz /= binnobj
for i in range(numZbins):
if stackedPdfs[:, i].sum():
bias_nz[i] -= np.average(redshiftGrid,
weights=stackedPdfs[:, i])
ind = binnobj > 0
bias_zmap /= binnobj
bias_zmean /= binnobj
print("")
print(' =======================================')
print(" ellSTD", ellPriorSigma,
"fluxError", extraFracFluxError,
"V_C", V_C, "zSTD", redshiftSigma)
cis_pdf, e = np.histogram(cis, 50, range=[0, 1])
cis_pdfcum = np.cumsum(cis_pdf) / np.sum(cis_pdf)
print("-------------------------------->> %.3g"
% (np.max(np.abs(np.abs(e[1:] - cis_pdfcum)))))
print(">>", end="")
for i in range(numZbins):
ind2 = zmeanBinLocs == i
if ind2.sum() > 2:
cis_pdf, e = np.histogram(cis[ind2], 50, range=[0, 1])
cis_pdfcum = np.cumsum(cis_pdf) / np.sum(cis_pdf)
print(" %.3g" % (np.max(np.abs(e[1:] - cis_pdfcum))),
end=" ")
# print("")
# print(' >>>> mean z bias %.3g'
# % np.abs(bias_zmean[ind]).mean(),
# 'mean N(z) bias %.3g' % np.abs(bias_nz[ind]).mean(), ' <<<<')
# print(' >>>> max z bias %.3g'
# % np.abs(bias_zmean[ind]).max(),
# 'max N(z) bias %.3g' % np.abs(bias_nz[ind]).max(), ' <<<<')
# print(' > bias_zmap : ',
# ' '.join(['%.3g' % x for x in bias_zmap]))
# print(' > z bias : ',
# ' '.join([('%.3g' % x) if np.isfinite(x)
# else '.' for x in bias_zmean]))
# print(' > nzbias : ',
# ' '.join([('%.3g' % x) if np.isfinite(x)
# else '.' for x in bias_nz]))
# print(' --------------------------------')
# for i in range(numConfLevels):
# print(' >', params['confidenceLevels'][i],
# ' :: ', ' '.join([('%.3g' % x) if np.isfinite(x)
# else '.' for x in confFractions[i, :]]))
# print(' =======================================')
|
ixkael/Delight
|
scripts/delight-optimize.py
|
Python
|
mit
| 9,708
|
[
"Galaxy"
] |
7ff608535b4ff5d848fe272447bbb95974ceb16699acd983001000bb7380d697
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# qooxdoo - the new era of web development
#
# http://qooxdoo.org
#
# Copyright:
# 2006-2013 1&1 Internet AG, Germany, http://www.1und1.de
#
# License:
# LGPL: http://www.gnu.org/licenses/lgpl.html
# EPL: http://www.eclipse.org/org/documents/epl-v10.php
# See the LICENSE file in the project's top-level directory for details.
#
# Authors:
# * Thomas Herchenroeder (thron7)
#
################################################################################
##
# A Mozilla Parser API / Esprima AST to tree1 transformer.
#
# https://developer.mozilla.org/en-US/docs/SpiderMonkey/Parser_API
##
import os, sys, re, types, copy
from ecmascript.frontend.treegenerator import method, symbol, symbol_base, SYMBOLS
from ecmascript.frontend import treegenerator, lang
from ecmascript.transform.optimizer import reducer
##
# The Mozilla tree is not normalized (i.e. there is no standard way to access
# children of a node), so there is no generic 'visit' method, only node
# type-specific methods.
#
class EsprimaToTree1(object):
def __init__(self, tree_root=None):
pass
def visit_Program(self, enode):
nnode = new_symbol('file', enode)
nnode.set("treegenerator_tag", 1)
s = new_symbol('statements', enode)
nnode.childappend(s)
# TODO: self.add_location(nnode, enode)
for child in enode["body"]:
nchild = self.visit_Statement(child)
if nchild:
s.childappend(nchild)
return nnode
def visit_Function(self, enode):
nnode = new_symbol('function', enode)
nnode.set("value", "function")
if enode["id"] != None:
id_node = new_symbol('identifier', enode)
id_node.set("value", enode["id"]['name'])
nnode.childappend(id_node)
# params
params_node = new_symbol('params', enode)
nnode.childappend(params_node)
for param in enode["params"]:
assert param['type'] == 'Identifier'
p_node = new_symbol('identifier', param)
p_node.set("value", param['name'])
params_node.childappend(p_node)
# body
body = new_symbol("body", enode["body"])
nnode.childappend(body)
nchild = getattr(self, "visit_"+enode["body"]["type"])(enode["body"]) # 'BlockStatement' or 'Expression'
body.childappend(nchild)
return nnode
##
# all the 'statement' types
def visit_Statement(self, enode):
return getattr(self, "visit_"+enode["type"])(enode)
def visit_EmptyStatement(self, enode):
return symbol('(empty)')()
def visit_BlockStatement(self, enode):
n = new_symbol("block", enode)
s = new_symbol("statements", enode)
n.childappend(s)
for child in enode["body"]:
nchild = self.visit_Statement(child)
if nchild:
s.childappend(nchild)
return n
def visit_ExpressionStatement(self, enode):
return self.visit_Expression(enode["expression"])
def visit_IfStatement(self, enode):
n = new_symbol("if", enode)
n.type = 'loop'
n.set('loopType', "IF")
n.set("value", "if")
# cond
n.childappend(self.visit_Expression(enode["test"]))
# then
b = new_symbol("body", enode["consequent"])
b.childappend(self.visit_Statement(enode["consequent"]))
n.childappend(b)
# else
if enode["alternate"] != None:
b = new_symbol("body", enode["alternate"])
b.childappend(self.visit_Statement(enode["alternate"]))
n.childappend(b)
return n
def visit_LabeledStatement(self, enode):
n = new_symbol("label", enode)
n.set("value", enode["label"])
n.childappend(self.visit_Statement(enode["body"]))
return n
def visit_BreakStatement(self, enode):
n = new_symbol("break", enode)
n.set("value", "break")
if enode["label"] != None:
n.childappend(self.visit_Identifier(enode["label"]))
return n
def visit_ContinueStatement(self, enode):
n = new_symbol("continue", enode)
n.set("value", "continue")
if enode["label"] != None:
n.childappend(self.visit_Identifier(enode["label"]))
return n
def visit_WithStatement(self, enode):
n = new_symbol("with", enode)
n.type = 'loop'
n.set('loopType', "WITH")
n.set("value", "with")
n.childappend(self.visit_Expression(enode["object"]))
n.childappend(self.visit_Statement(enode["body"]))
return n
def visit_SwitchStatement(self, enode):
n = new_symbol("switch", enode)
n.set("value", "switch")
n.childappend(self.visit_Expression(enode["discriminant"]))
b = new_symbol("body", enode)
n.childappend(b)
for child in enode["cases"]:
nchild = self.visit_SwitchCase(child)
if nchild:
b.childappend(nchild)
return n
def visit_ReturnStatement(self, enode):
n = new_symbol("return", enode)
n.set("value", "return")
if enode["argument"] != None:
n.childappend(self.visit_Expression(enode["argument"]))
return n
def visit_ThrowStatement(self, enode):
n = new_symbol("throw", enode)
n.set("value", "throw")
n.childappend(self.visit_Expression(enode["argument"]))
return n
def visit_TryStatement(self, enode):
n = new_symbol("try", enode)
n.set("value", "try")
n.childappend(self.visit_BlockStatement(enode["block"]))
# ALERT: This is Esprima; the Moz spec has 'handler' and 'guardedHandlers',
# Esprima uses 'handlers' and 'guardedHandlers' is always empty(!?)
for child in enode["handlers"]:
nchild = self.visit_CatchClause(child)
if nchild:
n.childappend(nchild)
break # tree1 only handles a single 'catch' clause; multiple 'catch' clauses are SpiderMonkey-specific
if enode["finalizer"] != None:
f = new_symbol("finally", enode["finalizer"])
f.set("value", "finally")
n.childappend(f)
f.childappend(self.visit_BlockStatement(enode["finalizer"]))
return n
def visit_WhileStatement(self, enode):
n = new_symbol("while", enode)
n.type = 'loop'
n.set("loopType", "WHILE")
n.set("value", "while")
n.childappend(self.visit_Expression(enode["test"])) # TODO: visit_Expression needs to return an expressionList!
b = new_symbol("body", enode["body"])
n.childappend(b)
b.childappend(self.visit_Statement(enode["body"]))
return n
def visit_DoWhileStatement(self, enode):
n = new_symbol("do", enode)
n.type = 'loop'
n.set("value", "do")
n.set("loopType", "DO")
b = new_symbol("body", enode)
n.childappend(b)
b.childappend(self.visit_Statement(enode["body"]))
n.childappend(self.visit_Expression(enode["test"]))
return n
def visit_ForStatement(self, enode): # for (;;)
n = new_symbol("for", enode)
n.type = 'loop'
n.set("value", "for")
n.set("loopType", "FOR")
n.set("forVariant", "iter")
cond = new_symbol("expressionList", enode)
n.childappend(cond)
# Condition
# first
f = new_symbol("first", enode)
cond.childappend(f)
el = new_symbol("expressionList", enode)
if enode['init'] == None:
pass
elif enode["init"]["type"] == "VariableDeclaration":
el.childappend(self.visit_VariableDeclaration(enode["init"]))
elif enode['init']['type'] == 'SequenceExpression':
el = self.visit_SequenceExpression(enode["init"]) # visit_SequenceExpression already creates an <expressionList>
else:
el.childappend(self.visit_Expression(enode["init"]))
f.childappend(el)
# second
s = new_symbol("second", enode)
cond.childappend(s)
el = new_symbol("expressionList", enode)
if enode["test"] == None:
pass
elif enode['test']['type'] == 'SequenceExpression':
el = self.visit_SequenceExpression(enode["test"]) # visit_SequenceExpression already creates an <expressionList>
else:
el.childappend(self.visit_Expression(enode["test"]))
s.childappend(el)
# third
t = new_symbol("third", enode)
cond.childappend(t)
el = new_symbol("expressionList", enode)
if enode["update"] == None:
pass
elif enode['update']['type'] == 'SequenceExpression':
el = self.visit_SequenceExpression(enode["update"]) # visit_SequenceExpression already creates an <expressionList>
else:
el.childappend(self.visit_Expression(enode["update"]))
t.childappend(el)
# body
b = new_symbol("body", enode['body'])
n.childappend(b)
b.childappend(self.visit_Statement(enode["body"]))
return n
def visit_ForInStatement(self, enode):
n = new_symbol("for", enode)
n.type = 'loop'
n.set("loopType", "FOR")
n.set("forVariant", "in")
n.set("value", "for")
i = new_symbol("operation", enode)
i.set("operator", "IN")
i.set("value", "in")
n.childappend(i)
if enode["left"]["type"] == "VariableDeclaration":
i.childappend(self.visit_VariableDeclaration(enode["left"]))
elif enode["left"]["type"] == "Expression":
i.childappend(self.visit_Expression(enode["left"]))
i.childappend(self.visit_Expression(enode["right"]))
# body
b = new_symbol("body", enode['body'])
n.childappend(b)
b.childappend(self.visit_Statement(enode["body"]))
return n
def visit_ForOfStatement(self, enode):
raise NotImplementedError("'for/of' statements are not yet supported")
def visit_LetStatement(self, enode):
raise NotImplementedError("'let' statements are not yet supported")
# Declarations are statements, too
def visit_FunctionDeclaration(self, enode):
assert enode["id"]
return self.visit_Function(enode)
def visit_VariableDeclaration(self, enode):
n = new_symbol("var", enode)
n.set("value", "var")
for child in enode["declarations"]:
n.childappend(self.visit_VariableDeclarator(child))
return n
def visit_VariableDeclarator(self, enode):
n = new_symbol("definition", enode)
if enode["init"]:
el = new_symbol("=", enode['id'])
el.type = "assignment"
el.set("operator", lang.TOKENS["="])
el.set("value", "=")
el.childappend(self.visit_Identifier(enode["id"]))
el.childappend(self.visit_Expression(enode["init"]))
else:
el = self.visit_Identifier(enode["id"])
n.childappend(el)
return n
# Expressions
def visit_Expression(self, enode):
return getattr(self, "visit_"+enode["type"])(enode)
def visit_ThisExpression(self, enode):
# convert to simple 'this' identifier
m = copy.deepcopy(enode)
m['type'] = 'Identifier'
m['name'] = 'this'
n = self.visit_Identifier(m)
return n
def visit_ArrayExpression(self, enode): # array literal
n = new_symbol("array", enode)
for child in enode["elements"]:
if child is None:
n.childappend(symbol("(empty)")())
else:
n.childappend(self.visit_Expression(child))
return n
def visit_ObjectExpression(self, enode): # map
n = new_symbol("map", enode)
for child in enode["properties"]:
item = new_symbol("keyvalue", child)
n.childappend(item)
# key
if child['key']['type'] == 'Literal':
if isinstance(child['key']['value'], types.StringTypes):
item.set("key", child['key']['value'])
item.set("quote", "doublequotes") # TODO: the 'raw' member includes the actual quotes
else: # Number
item.set("key", str(child['key']['value']))
item.set("quote", "")
else: # 'Identifier'
item.set("key", child['key']['name'])
# value
val = new_symbol("value", child['value'])
item.childappend(val)
val.childappend(self.visit_Expression(child['value']))
return n
def visit_FunctionExpression(self, enode):
return self.visit_Function(enode)
def visit_ArrowExpression(self, enode):
raise NotImplementedError("'arrow' expressions are not yet supported")
def visit_SequenceExpression(self, enode): # '1,2,3;'
n = new_symbol("expressionList", enode)
for child in enode["expressions"]:
n.childappend(self.visit_Expression(child))
return n
def visit_UnaryExpression(self, enode): # -, +, !, ~, typeof, void, delete
n = new_symbol(enode["operator"], enode)
n.type = "operation"
try:
n.set("operator", lang.TOKENS[enode["operator"]]) # -, +, ..
except KeyError:
n.set("operator", lang.RESERVED[enode["operator"]]) # typeof, void, delete
n.set("value", enode["operator"])
if enode["prefix"]:
n.set("left", "true")
n.childappend(self.visit_Expression(enode["argument"]))
return n
def visit_BinaryExpression(self, enode): # <, <=, ...
n = new_symbol(enode["operator"], enode)
n.type = "operation"
try:
n.set("operator", lang.TOKENS[enode["operator"]]) # <, <=, ...
except KeyError:
n.set("operator", lang.RESERVED[enode["operator"]]) # instanceof
n.set("value", enode["operator"])
n.childappend(self.visit_Expression(enode["left"]))
n.childappend(self.visit_Expression(enode["right"]))
return n
def visit_AssignmentExpression(self, enode): # =, +=, ...
n = new_symbol(enode["operator"], enode)
n.type = "assignment"
n.set("value", enode["operator"])
n.set("operator", lang.TOKENS[enode["operator"]])
n.childappend(self.visit_Expression(enode["left"]))
n.childappend(self.visit_Expression(enode["right"]))
return n
def visit_UpdateExpression(self, enode): # --, ++
n = new_symbol(enode["operator"], enode)
n.type = "operation"
n.set("operator", lang.TOKENS[enode["operator"]])
n.set("value", enode["operator"])
if enode["prefix"]:
n.set("left", "true")
n.childappend(self.visit_Expression(enode["argument"]))
return n
def visit_LogicalExpression(self, enode): # ||, &&
n = new_symbol(enode["operator"], enode)
n.type = "operation"
n.set("operator", lang.TOKENS[enode["operator"]])
n.set("value", enode["operator"])
n.childappend(self.visit_Expression(enode["left"]))
n.childappend(self.visit_Expression(enode["right"]))
return n
def visit_ConditionalExpression(self, enode): # .. ? .. : .. (hook)
n = new_symbol("?", enode)
n.type = "operation"
n.set("operator", lang.TOKENS["?"])
n.set("value", "?")
n.childappend(self.visit_Expression(enode["test"]))
n.childappend(self.visit_Expression(enode["consequent"]))
n.childappend(self.visit_Expression(enode["alternate"]))
return n
def visit_NewExpression(self, enode):
n = new_symbol("operation", enode)
n.set("operator", "NEW")
n.set("value", "new")
if enode["arguments"]: # have to coerce two members into a single 'call' tree
arg = new_symbol("call", enode['callee'])
arg.set("value", "(")
operand = new_symbol("operand", enode['callee'])
operand.childappend(self.visit_Expression(enode["callee"]))
arg.childappend(operand)
cargs = new_symbol("arguments", enode['callee'])
for child in enode["arguments"]:
cargs.childappend(self.visit_Expression(child))
arg.childappend(cargs)
else:
arg = self.visit_Expression(enode["callee"])
n.childappend(arg)
return n
def visit_CallExpression(self, enode): # 'foo()'
n = new_symbol("call", enode)
operand = new_symbol("operand", enode)
operand.childappend(self.visit_Expression(enode["callee"]))
n.childappend(operand)
params = new_symbol("arguments", enode)
n.childappend(params)
for child in enode["arguments"]:
nchild = self.visit_Expression(child)
params.childappend(nchild)
return n
def visit_MemberExpression(self, enode): # 'a.b', 'a[b]'
if enode["computed"]: # a[b]
n = new_symbol("accessor", enode)
n.set("value", "[")
else: # a.b
n = new_symbol("dotaccessor", enode)
n.set("value", ".")
# left/object
n.childappend(self.visit_Expression(enode["object"]))
# right/property
if enode["computed"]:
key = new_symbol("key", enode)
n.childappend(key)
p = key
else:
p = n
if enode["property"]["type"] == 'Identifier':
p.childappend(self.visit_Identifier(enode["property"]))
else:
p.childappend(self.visit_Expression(enode["property"]))
return n
def visit_YieldExpression(self, enode):
raise NotImplementedError("'yield' expressions are not yet supported")
def visit_ComprehensionExpression(self, enode):
raise NotImplementedError("'comprehension' expressions are not yet supported")
def visit_GeneratorExpression(self, enode):
raise NotImplementedError("'generator' expressions are not yet supported")
def visit_GraphExpression(self, enode):
raise NotImplementedError("'graph' expressions are not yet supported")
def visit_GraphIndexExpression(self, enode):
raise NotImplementedError("'graph index' expressions are not yet supported")
def visit_LetExpression(self, enode):
raise NotImplementedError("'let' expressions are not yet supported")
# Patterns (destructuring assignment and binding forms)
# TBD
# Clauses
def visit_SwitchCase(self, enode):
if enode["test"] != None:
n = new_symbol("case", enode)
n.childappend(self.visit_Expression(enode["test"]))
else:
n = new_symbol("default", enode)
stmts = new_symbol("statements", enode)
n.childappend(stmts)
for child in enode["consequent"]:
stmts.childappend(self.visit_Statement(child))
return n
def visit_CatchClause(self, enode):
n = new_symbol("catch", enode)
n.set("value", "catch")
p = new_symbol("params", enode['param'])
n.childappend(p)
p.childappend(self.visit_Identifier(enode["param"])) # Moz API has "Pattern" i.p.o. Identifier
# Skipped: enode["guard", spidermonkey-specific
n.childappend(self.visit_BlockStatement(enode["body"]))
return n
def visit_ComprehensionBlock(self, enode):
raise NotImplementedError("'comprehension' blocks are not yet supported")
def visit_Identifier(self, enode):
n = new_symbol("identifier", enode)
n.set("value", enode["name"])
return n
def visit_Literal(self, enode):
n = new_symbol("constant", enode)
# have to sort out RegExp literals
if enode["value"] == {}:
# Esprima 1.0.4 represents regexp's as empty map in Json!, so i have
# to fall back to the "raw" property.
# the online demo esprima.org/demo/parse.html has the regex as a
# string in "value" directly!?
n = treegenerator.parse(enode["raw"], expr=True) # need esparse --raw here!!
else:
n = reducer.set_node_type_from_value(n, enode["value"])
return n
# - -- helpers ----------------------------------------------------------------
def new_symbol(typ, enode):
loc = enode['loc']['start']
n = symbol(typ)(loc['line'], loc['column']+1)
return n
# - ---------------------------------------------------------------------------
def esprima_to_tree1(etree):
tree_transformer = EsprimaToTree1(etree)
new_node = tree_transformer.visit_Program(etree)
return new_node
|
sebastienhupin/qxrad
|
qooxdoo/tool/pylib/ecmascript/transform/moztree_to_tree1.py
|
Python
|
lgpl-3.0
| 21,023
|
[
"VisIt"
] |
98f9044e89b049165ac0c6605ab1a439763bc1e184cafcd549a64ccd1de7d510
|
import numpy as np
from gpaw.overlap import Overlap
from gpaw.fd_operators import Laplace
from gpaw.lfc import LocalizedFunctionsCollection as LFC
from gpaw.utilities import unpack
from gpaw.io import FileReference
from gpaw.lfc import BasisFunctions
from gpaw.utilities.blas import axpy
from gpaw.transformers import Transformer
from gpaw.fd_operators import Gradient
from gpaw.band_descriptor import BandDescriptor
from gpaw import extra_parameters
from gpaw.wavefunctions.fdpw import FDPWWaveFunctions
from gpaw.hs_operators import MatrixOperator
from gpaw.preconditioner import Preconditioner
from gpaw.kpt_descriptor import KPointDescriptor
from gpaw.kpoint import KPoint
from gpaw.mpi import serial_comm
class FDWaveFunctions(FDPWWaveFunctions):
def __init__(self, stencil, diagksl, orthoksl, initksl,
gd, nvalence, setups, bd,
dtype, world, kd, timer=None):
FDPWWaveFunctions.__init__(self, diagksl, orthoksl, initksl,
gd, nvalence, setups, bd,
dtype, world, kd, timer)
# Kinetic energy operator:
self.kin = Laplace(self.gd, -0.5, stencil, self.dtype)
self.matrixoperator = MatrixOperator(self.orthoksl)
def empty(self, n=(), dtype=float, global_array=False, realspace=False):
return self.gd.empty(n, dtype, global_array)
def integrate(self, a_xg, b_yg=None, global_integral=True):
return self.gd.integrate(a_xg, b_yg, global_integral)
def bytes_per_wave_function(self):
return self.gd.bytecount(self.dtype)
def set_setups(self, setups):
self.pt = LFC(self.gd, [setup.pt_j for setup in setups],
self.kd, dtype=self.dtype, forces=True)
FDPWWaveFunctions.set_setups(self, setups)
def set_positions(self, spos_ac):
FDPWWaveFunctions.set_positions(self, spos_ac)
def summary(self, fd):
fd.write('Wave functions: Uniform real-space grid\n')
fd.write('Kinetic energy operator: %s\n' % self.kin.description)
def make_preconditioner(self, block=1):
return Preconditioner(self.gd, self.kin, self.dtype, block)
def apply_pseudo_hamiltonian(self, kpt, hamiltonian, psit_xG, Htpsit_xG):
self.timer.start('Apply hamiltonian')
self.kin.apply(psit_xG, Htpsit_xG, kpt.phase_cd)
hamiltonian.apply_local_potential(psit_xG, Htpsit_xG, kpt.s)
self.timer.stop('Apply hamiltonian')
def add_orbital_density(self, nt_G, kpt, n):
if self.dtype == float:
axpy(1.0, kpt.psit_nG[n]**2, nt_G)
else:
axpy(1.0, kpt.psit_nG[n].real**2, nt_G)
axpy(1.0, kpt.psit_nG[n].imag**2, nt_G)
def add_to_density_from_k_point_with_occupation(self, nt_sG, kpt, f_n):
# Used in calculation of response part of GLLB-potential
nt_G = nt_sG[kpt.s]
if self.dtype == float:
for f, psit_G in zip(f_n, kpt.psit_nG):
axpy(f, psit_G**2, nt_G)
else:
for f, psit_G in zip(f_n, kpt.psit_nG):
axpy(f, psit_G.real**2, nt_G)
axpy(f, psit_G.imag**2, nt_G)
# Hack used in delta-scf calculations:
if hasattr(kpt, 'c_on'):
assert self.bd.comm.size == 1
d_nn = np.zeros((self.bd.mynbands, self.bd.mynbands),
dtype=complex)
for ne, c_n in zip(kpt.ne_o, kpt.c_on):
d_nn += ne * np.outer(c_n.conj(), c_n)
for d_n, psi0_G in zip(d_nn, kpt.psit_nG):
for d, psi_G in zip(d_n, kpt.psit_nG):
if abs(d) > 1.e-12:
nt_G += (psi0_G.conj() * d * psi_G).real
def calculate_kinetic_energy_density(self, grad_v):
assert not hasattr(self.kpt_u[0], 'c_on')
if isinstance(self.kpt_u[0].psit_nG, FileReference):
raise RuntimeError('Wavefunctions have not been initialized.')
taut_sG = self.gd.zeros(self.nspins)
dpsit_G = self.gd.empty(dtype=self.dtype)
for kpt in self.kpt_u:
for f, psit_G in zip(kpt.f_n, kpt.psit_nG):
for v in range(3):
grad_v[v](psit_G, dpsit_G, kpt.phase_cd)
axpy(0.5 * f, abs(dpsit_G)**2, taut_sG[kpt.s])
self.kpt_comm.sum(taut_sG)
self.band_comm.sum(taut_sG)
return taut_sG
def ibz2bz(self, atoms):
"""Transform wave functions in IBZ to the full BZ."""
assert self.kd.comm.size == 1
# New k-point descriptor for full BZ:
kd = KPointDescriptor(self.kd.bzk_kc, nspins=self.nspins)
kd.set_symmetry(atoms, self.setups, usesymm=None)
kd.set_communicator(serial_comm)
self.pt = LFC(self.gd, [setup.pt_j for setup in self.setups],
kd, dtype=self.dtype)
self.pt.set_positions(atoms.get_scaled_positions())
self.initialize_wave_functions_from_restart_file()
weight = 2.0 / kd.nspins / kd.nbzkpts
# Build new list of k-points:
kpt_u = []
for s in range(self.nspins):
for k in range(kd.nbzkpts):
# Index of symmetry related point in the IBZ
ik = self.kd.bz2ibz_k[k]
r, u = self.kd.get_rank_and_index(s, ik)
assert r == 0
kpt = self.kpt_u[u]
phase_cd = np.exp(2j * np.pi * self.gd.sdisp_cd *
kd.bzk_kc[k, :, np.newaxis])
# New k-point:
kpt2 = KPoint(weight, s, k, k, phase_cd)
kpt2.f_n = kpt.f_n / kpt.weight / kd.nbzkpts * 2 / self.nspins
kpt2.eps_n = kpt.eps_n.copy()
# Transform wave functions using symmetry operation:
Psit_nG = self.gd.collect(kpt.psit_nG)
if Psit_nG is not None:
Psit_nG = Psit_nG.copy()
for Psit_G in Psit_nG:
Psit_G[:] = self.kd.transform_wave_function(Psit_G, k)
kpt2.psit_nG = self.gd.empty(self.bd.nbands, dtype=self.dtype)
self.gd.distribute(Psit_nG, kpt2.psit_nG)
# Calculate PAW projections:
kpt2.P_ani = self.pt.dict(len(kpt.psit_nG))
self.pt.integrate(kpt2.psit_nG, kpt2.P_ani, k)
kpt_u.append(kpt2)
self.kd = kd
self.kpt_u = kpt_u
def write(self, writer, write_wave_functions=False):
writer['Mode'] = 'fd'
if not write_wave_functions:
return
writer.add('PseudoWaveFunctions',
('nspins', 'nibzkpts', 'nbands',
'ngptsx', 'ngptsy', 'ngptsz'),
dtype=self.dtype)
if hasattr(writer, 'hdf5'):
parallel = (self.world.size > 1)
for kpt in self.kpt_u:
indices = [kpt.s, kpt.k]
indices.append(self.bd.get_slice())
indices += self.gd.get_slice()
writer.fill(kpt.psit_nG, parallel=parallel, *indices)
else:
for s in range(self.nspins):
for k in range(self.nibzkpts):
for n in range(self.bd.nbands):
psit_G = self.get_wave_function_array(n, k, s)
writer.fill(psit_G, s, k, n)
def initialize_from_lcao_coefficients(self, basis_functions, mynbands):
for kpt in self.kpt_u:
kpt.psit_nG = self.gd.zeros(self.bd.mynbands, self.dtype)
basis_functions.lcao_to_grid(kpt.C_nM,
kpt.psit_nG[:mynbands], kpt.q)
kpt.C_nM = None
def random_wave_functions(self, nao):
"""Generate random wave functions."""
gpts = self.gd.N_c[0]*self.gd.N_c[1]*self.gd.N_c[2]
if self.bd.nbands < gpts/64:
gd1 = self.gd.coarsen()
gd2 = gd1.coarsen()
psit_G1 = gd1.empty(dtype=self.dtype)
psit_G2 = gd2.empty(dtype=self.dtype)
interpolate2 = Transformer(gd2, gd1, 1, self.dtype).apply
interpolate1 = Transformer(gd1, self.gd, 1, self.dtype).apply
shape = tuple(gd2.n_c)
scale = np.sqrt(12 / abs(np.linalg.det(gd2.cell_cv)))
old_state = np.random.get_state()
np.random.seed(4 + self.world.rank)
for kpt in self.kpt_u:
for psit_G in kpt.psit_nG[nao:]:
if self.dtype == float:
psit_G2[:] = (np.random.random(shape) - 0.5) * scale
else:
psit_G2.real = (np.random.random(shape) - 0.5) * scale
psit_G2.imag = (np.random.random(shape) - 0.5) * scale
interpolate2(psit_G2, psit_G1, kpt.phase_cd)
interpolate1(psit_G1, psit_G, kpt.phase_cd)
np.random.set_state(old_state)
elif gpts/64 <= self.bd.nbands < gpts/8:
gd1 = self.gd.coarsen()
psit_G1 = gd1.empty(dtype=self.dtype)
interpolate1 = Transformer(gd1, self.gd, 1, self.dtype).apply
shape = tuple(gd1.n_c)
scale = np.sqrt(12 / abs(np.linalg.det(gd1.cell_cv)))
old_state = np.random.get_state()
np.random.seed(4 + self.world.rank)
for kpt in self.kpt_u:
for psit_G in kpt.psit_nG[nao:]:
if self.dtype == float:
psit_G1[:] = (np.random.random(shape) - 0.5) * scale
else:
psit_G1.real = (np.random.random(shape) - 0.5) * scale
psit_G1.imag = (np.random.random(shape) - 0.5) * scale
interpolate1(psit_G1, psit_G, kpt.phase_cd)
np.random.set_state(old_state)
else:
shape = tuple(self.gd.n_c)
scale = np.sqrt(12 / abs(np.linalg.det(self.gd.cell_cv)))
old_state = np.random.get_state()
np.random.seed(4 + self.world.rank)
for kpt in self.kpt_u:
for psit_G in kpt.psit_nG[nao:]:
if self.dtype == float:
psit_G[:] = (np.random.random(shape) - 0.5) * scale
else:
psit_G.real = (np.random.random(shape) - 0.5) * scale
psit_G.imag = (np.random.random(shape) - 0.5) * scale
np.random.set_state(old_state)
def estimate_memory(self, mem):
FDPWWaveFunctions.estimate_memory(self, mem)
|
ajylee/gpaw-rtxs
|
gpaw/wavefunctions/fd.py
|
Python
|
gpl-3.0
| 10,754
|
[
"GPAW"
] |
e3ee5c75e80d9277444d0d95ebc35014236ae280f93b56ad03426c7ee9b899ac
|
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
from skbio.alignment._ssw._ssw_wrapper import (
StripedSmithWaterman, local_pairwise_align_ssw, AlignmentStructure)
__all__ = ['StripedSmithWaterman', 'AlignmentStructure',
'local_pairwise_align_ssw']
from numpy.testing import Tester
test = Tester().test
|
JWDebelius/scikit-bio
|
skbio/alignment/_ssw/__init__.py
|
Python
|
bsd-3-clause
| 628
|
[
"scikit-bio"
] |
d55c5fa9fd005dc78232ae2ffdf2a691ce08a5a050c27c0e0a6539430382bffd
|
"""
Histogram vs Kernel Density Estimation
--------------------------------------
Figure 6.1
Density estimation using histograms and kernels. The top panels show two
histogram representations of the same data (shown by plus signs in the bottom
of each panel) using the same bin width, but with the bin centers of the
histograms offset by 0.25. The middle-left panel shows an adaptive histogram
where each bin is centered on an individual point and these bins can overlap.
This adaptive representation preserves the bimodality of the data. The
remaining panels show kernel density estimation using Gaussian kernels with
different bandwidths, increasing from the middle-right panel to the
bottom-right, and with the largest bandwidth in the bottom-left panel. The
trade-off of variance for bias becomes apparent as the bandwidth of the
kernels increases.
"""
# Author: Jake VanderPlas
# License: BSD
# The figure produced by this code is published in the textbook
# "Statistics, Data Mining, and Machine Learning in Astronomy" (2013)
# For more information, see http://astroML.github.com
# To report a bug or issue, use the following forum:
# https://groups.google.com/forum/#!forum/astroml-general
import numpy as np
from matplotlib import pyplot as plt
from scipy import stats
#----------------------------------------------------------------------
# This function adjusts matplotlib settings for a uniform feel in the textbook.
# Note that with usetex=True, fonts are rendered with LaTeX. This may
# result in an error if LaTeX is not installed on your system. In that case,
# you can set usetex to False.
from astroML.plotting import setup_text_plots
setup_text_plots(fontsize=8, usetex=True)
#------------------------------------------------------------
# Draw the random data
np.random.seed(1)
x = np.concatenate([np.random.normal(-0.5, 0.3, size=14),
np.random.normal(1, 0.3, size=7)])
#------------------------------------------------------------
# First figure: silly histogram binning
fig1 = plt.figure(figsize=(5, 3))
fig1.subplots_adjust(left=0.12, right=0.95, wspace=0.05,
bottom=0.15, top=0.9, hspace=0.05)
FC = '#6666FF'
XLIM = (-2, 2.9)
YLIM = (-0.09, 1.1)
ax = fig1.add_subplot(121)
bins = np.linspace(-1.8, 2.7, 13)
ax.hist(x, bins=bins, normed=True,
histtype='stepfilled', fc='k', alpha=0.3)
ax.plot(XLIM, [0, 0], '-k', lw=1)
ax.plot(x, 0 * x - 0.05, '+k')
ax.set_xlim(XLIM)
ax.set_ylim(YLIM)
ax.set_xlabel('$x$')
ax.set_ylabel('$p(x)$')
ax = fig1.add_subplot(122)
ax.yaxis.set_major_formatter(plt.NullFormatter())
ax.hist(x, bins=bins + 0.25, normed=True,
histtype='stepfilled', fc='k', alpha=0.3)
ax.plot(XLIM, [0, 0], '-k', lw=1)
ax.plot(x, 0 * x - 0.05, '+k')
ax.set_xlim(XLIM)
ax.set_ylim(YLIM)
ax.set_xlabel('$x$')
#------------------------------------------------------------
# First figure: transition to KDE
fig2 = plt.figure(figsize=(5, 5))
fig2.subplots_adjust(left=0.12, right=0.95, wspace=0.05,
bottom=0.1, top=0.95, hspace=0.05)
ax = fig2.add_subplot(221)
ax.xaxis.set_major_formatter(plt.NullFormatter())
binwidth = bins[1] - bins[0]
x_plot = np.linspace(-4, 4, 1000)
y_plot = (abs(x_plot - x[:, None]) <= 0.5 * binwidth).astype(float)
y_plot /= (binwidth * len(x))
ax.fill(x_plot, y_plot.sum(0), ec='k', lw=1, fc='k', alpha=0.3)
ax.plot(x_plot, y_plot.T, '-k', lw=1)
ax.plot(x, 0 * x - 0.05, '+k')
ax.set_xlim(XLIM)
ax.set_ylim(YLIM)
ax.set_ylabel('$p(x)$')
ax = fig2.add_subplot(222)
ax.xaxis.set_major_formatter(plt.NullFormatter())
ax.yaxis.set_major_formatter(plt.NullFormatter())
binwidth = bins[1] - bins[0]
x_plot = np.linspace(-4, 4, 1000)
y_plot = binwidth * stats.norm.pdf(x_plot, x[:, None], 0.1)
y_plot /= (binwidth * len(x))
ax.fill(x_plot, y_plot.sum(0), ec='k', lw=1, fc='k', alpha=0.3)
ax.plot(x_plot, y_plot.T, '-k', lw=1)
ax.plot(x, 0 * x - 0.05, '+k')
ax.set_xlim(XLIM)
ax.set_ylim(YLIM)
ax = fig2.add_subplot(223)
binwidth = bins[1] - bins[0]
x_plot = np.linspace(-4, 4, 1000)
y_plot = binwidth * stats.norm.pdf(x_plot, x[:, None], 0.7)
y_plot /= (binwidth * len(x))
ax.fill(x_plot, y_plot.sum(0), ec='k', lw=1, fc='k', alpha=0.3)
ax.plot(x_plot, 4 * y_plot.T, '-k', lw=1)
ax.plot(x, 0 * x - 0.05, '+k')
ax.set_xlim(XLIM)
ax.set_ylim(YLIM)
ax.set_ylabel('$p(x)$')
ax.set_xlabel('$x$')
ax = fig2.add_subplot(224)
ax.yaxis.set_major_formatter(plt.NullFormatter())
binwidth = bins[1] - bins[0]
x_plot = np.linspace(-4, 4, 1000)
y_plot = binwidth * stats.norm.pdf(x_plot, x[:, None], 0.2)
y_plot /= (binwidth * len(x))
ax.fill(x_plot, y_plot.sum(0), ec='k', lw=1, fc='k', alpha=0.3)
ax.plot(x_plot, y_plot.T, '-k', lw=1)
ax.plot(x, 0 * x - 0.05, '+k')
ax.set_xlim(XLIM)
ax.set_ylim(YLIM)
ax.set_xlabel('$x$')
plt.show()
|
eramirem/astroML
|
book_figures/chapter6/fig_hist_to_kernel.py
|
Python
|
bsd-2-clause
| 4,774
|
[
"Gaussian"
] |
0599c3be018b6e1b33f4dd8bfe87c23890ba81c83ef11d455f73da4288ff930e
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2012 Jared Boone
#
# This file is part of HackRF.
#
# This is a free hardware design; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This design is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this design; see the file COPYING. If not, write to
# the Free Software Foundation, Inc., 51 Franklin Street,
# Boston, MA 02110-1301, USA.
#
# This program configures a Silicon Labs Si5351C clock generation IC
# via an I2C interface, using a Dangerous Prototypes Bus Pirate v3.5
# and the pyBusPirateLite Python library.
#
# Si5351C:
# http://www.silabs.com/products/clocksoscillators/clock-generators-and-buffers/Pages/clock+vcxo.aspx
# Bus Pirate:
# http://dangerousprototypes.com/docs/Bus_Pirate
# pyBusPirateLite:
# http://code.google.com/p/the-bus-pirate/
#
# This Si5351C configuration is a work in progress, it does not yet
# implement the clock plan described in the HackRF wiki:
# https://github.com/mossmann/hackrf/wiki/Clocking
#
# To follow progress in configuring the Si5351C, please refer to the
# HackRF wiki:
# https://github.com/mossmann/hackrf/wiki/Lemondrop-Bring-Up
import sys
from pyBusPirateLite.I2C import *
from math import log
if len(sys.argv) < 2:
print('Usage: %s <path to serial device>' % (sys.argv[0],))
sys.exit()
serial_path = sys.argv[1]
print('Connecting to Bus Pirate on "%s"...' % (serial_path,))
i2c = I2C(serial_path, 115200)
i2c.resetBP()
print('Entering I2C mode...')
if not i2c.BBmode():
print('BBmode() failed')
sys.exit()
if not i2c.enter_I2C():
print('enter_I2C() failed')
sys.exit()
if not i2c.set_speed(I2CSpeed._400KHZ):
print('set_speed() failed')
sys.exit()
i2c.cfg_pins(I2CPins.POWER)
i2c.timeout(0.2)
def write_registers(first_register_number, values):
data = [0xC0, first_register_number]
if isinstance(values, (list, tuple)):
data.extend(values)
else:
data.append(values)
i2c.send_start_bit()
i2c.bulk_trans(len(data), data)
i2c.send_stop_bit()
# r is the R output divider (should be 1, 2, 4, 8. . .)
# note: si5351c.c's r parameter is encoded (log not taken)
# use p2=0 and p3=1 for integer mode
def set_multisynth_parameters(ms_n, p1, p2, p3, r):
register_number = 42 + (ms_n * 8)
values = (
(p3 >> 8) & 0xFF,
(p3 >> 0) & 0xFF,
(int(log(r, 2)) << 4) | (0 << 2) | ((p1 >> 16) & 0x3),
(p1 >> 8) & 0xFF,
(p1 >> 0) & 0xFF,
(((p3 >> 16) & 0xF) << 4) | (((p2 >> 16) & 0xF) << 0),
(p2 >> 8) & 0xFF,
(p2 >> 0) & 0xFF
)
write_registers(register_number, values)
# Get the appropriate P1 setting for a given frequency.
# Assumes VCO is 800 MHz and you want integer division and R=4.
def integer_p1(frequency):
return int(800e6/frequency) * 128 - 512
def set_codec_rate(frequency):
set_multisynth_parameters(1, integer_p1(frequency * 4), 0, 1, 4)
print('Configuring Si5351...')
# Disable all CLKx outputs.
write_registers(3, 0xFF)
# Turn off OEB pin control for all CLKx
write_registers(9, 0xFF)
# Power down all CLKx
write_registers(16, (0x80, 0x80, 0x80, 0x80, 0x80, 0x80, 0xC0, 0xC0))
# Register 183: Crystal Internal Load Capacitance
# Reads as 0xE4 on power-up
# Set to 10pF (until I find out what loading the crystal/PCB likes best)
write_registers(183, 0xE4)
# Register 187: Fanout Enable
# Turn on XO and MultiSynth fanout only.
write_registers(187, 0x50)
# Register 15: PLL Input Source
# CLKIN_DIV=0 (Divide by 1)
# PLLB_SRC=0 (XTAL input)
# PLLA_SRC=0 (XTAL input)
write_registers(15, 0x00)
# MultiSynth NA (PLL1)
write_registers(26, (0x00, 0x01, 0x00, 0x0E, 0x00, 0x00, 0x00, 0x00))
# MultiSynth NB (PLL2)
###
# MultiSynth 0
# This is the source for the MAX2837 clock input.
# It is also used to generate the ADC/DAC clocks.
set_multisynth_parameters(0, integer_p1(80e6), 0, 1, 2) # 40MHz with R=2
# MultiSynth 1 (MAX5864 and CPLD)
#set_codec_rate(20e6)
set_multisynth_parameters(1, integer_p1(80e6), 0, 1, 4) # 20MHz with R=2
# MultiSynth 2 (CPLD)
set_multisynth_parameters(2, integer_p1(80e6), 0, 1, 1) # 20MHz with R=2
# MultiSynth 3 (CPLD)
set_multisynth_parameters(3, integer_p1(80e6), 0, 1, 1) # 20MHz with R=2
# MultiSynth 4
# This is the source for the LPC43xx external clock input.
set_multisynth_parameters(4, 8021, 1, 3, 1) # 12MHz
#set_multisynth_parameters(4, integer_p1(20e6), 0, 1, 1) # 20 MHz
#set_multisynth_parameters(4, integer_p1(80e6), 0, 1, 4) # 20 MHz using R=4
#set_multisynth_parameters(4, 3584, 0, 1, 1) # 25MHz
# MultiSynth 6/7 R dividers
write_registers(92, 0x00)
# Registers 16 through 23: CLKx Control
# CLK0:
# CLK0_PDN=0 (powered up)
# MS0_INT=1 (integer mode)
# MS0_SRC=0 (PLLA as source for MultiSynth 0)
# CLK0_INV=0 (not inverted)
# CLK0_SRC=3 (MS0 as input source)
# CLK0_IDRV=3 (8mA)
# CLK1:
# CLK1_PDN=0 (powered up)
# MS1_INT=1 (integer mode)
# MS1_SRC=0 (PLLA as source for MultiSynth 1)
# CLK1_INV=0 (not inverted)
# CLK1_SRC=2 (MS0 as input source)
# CLK1_IDRV=3 (8mA)
# CLK2:
# CLK2_PDN=0 (powered up)
# MS2_INT=1 (integer mode)
# MS2_SRC=0 (PLLA as source for MultiSynth 1)
# CLK2_INV=0 (not inverted)
# CLK2_SRC=2 (MS0 as input source)
# CLK2_IDRV=3 (8mA)
# CLK3:
# CLK3_PDN=0 (powered up)
# MS3_INT=1 (integer mode)
# MS3_SRC=0 (PLLA as source for MultiSynth 1)
# CLK3_INV=0 (not inverted)
# CLK3_SRC=2 (MS0 as input source)
# CLK3_IDRV=3 (8mA)
# CLK4:
# CLK4_PDN=0 (powered up)
# MS4_INT=0 (fractional mode -- to support 12MHz to LPC for USB DFU)
# MS4_SRC=0 (PLLA as source for MultiSynth 4)
# CLK4_INV=0 (not inverted)
# CLK4_SRC=3 (MS4 as input source)
# CLK4_IDRV=3 (8mA)
write_registers(16, (0x4F, 0x4B, 0x4B, 0x4B, 0x0F, 0x80, 0xC0, 0xC0))
# Enable CLK outputs 0, 1, 4 only.
write_registers(3, 0xFF ^ 0b00011111)
raw_input("<return> to quit...")
print('Powering down...')
i2c.cfg_pins(0)
|
pavsa/hackrf-spectrum-analyzer
|
src/hackrf-sweep/lib/hackrf/hardware/test/si5351-configure.py
|
Python
|
gpl-3.0
| 6,337
|
[
"CRYSTAL"
] |
ab4720459622ba195c70a0883df772a32f4aa90278cb925832679736035be3f1
|
#!/usr/bin/env python
import os.path, sys
import tornado.auth
import tornado.httpserver
import tornado.ioloop
import tornado.options
import tornado.web
from tornado import gen
from tornado.web import asynchronous
from threading import Thread
from functools import wraps
import chancecoind
from lib import (config, util, exceptions, bitcoin, blocks)
from lib import (send, order, btcpay, bet, burn, cancel)
db = None
is_bitcoind_connected = True
try:
chancecoind.set_options()
db = util.connect_to_db()
except exceptions.ConfigurationError:
pass
def bet_tuples(bets):
bets_new = []
if bets!=None:
for bet in bets:
bets_new.append((bet['source'],util.devise(db, bet['bet'], 'CHA', 'output'),bet['chance'],bet['payout'],util.devise(db, bet['profit'], 'CHA', 'output')))
return bets_new
def balance_tuples(balances):
balances_new = []
if balances!=None:
cha_supply = util.cha_supply(db)
for balance in balances:
burns = util.get_burns(db, source = balance['address'], validity='valid')
burned = sum([burn['burned'] for burn in burns])
balances_new.append((balance['address'],util.devise(db, balance['amount'], 'CHA', 'output'),util.devise(db, burned, 'BTC', 'output'), balance['amount']/cha_supply*100))
return balances_new
def order_tuples(orders):
orders_new = []
if orders!=None:
for order in orders:
if order['get_asset']=='CHA':
cha_side = 'get_amount'
btc_side = 'give_amount'
buysell = 'buy'
else:
cha_side = 'give_amount'
btc_side = 'get_amount'
buysell = 'sell'
orders_new.append((util.devise(db, order[cha_side], 'CHA', 'output'),float(util.devise(db, order[btc_side], 'BTC', 'output'))/float(util.devise(db, order[cha_side], 'CHA', 'output')), util.devise(db, order[btc_side], 'BTC', 'output'), buysell, order['tx_hash']))
return orders_new
def order_match_tuples(order_matches):
order_matches_new = []
if order_matches!=None:
for order_match in order_matches:
if order_match['forward_asset']=='BTC':
btc = util.devise(db, order_match['forward_amount'], 'BTC', 'output')
cha = util.devise(db, order_match['backward_amount'], 'CHA', 'output')
else:
btc = util.devise(db, order_match['backward_amount'], 'BTC', 'output')
cha = util.devise(db, order_match['forward_amount'], 'CHA', 'output')
order_matches_new.append((btc,cha,order_match['id']))
return order_matches_new
def run_async(func):
@wraps(func)
def async_func(*args, **kwargs):
func_hl = Thread(target = func, args = args, kwargs = kwargs)
func_hl.start()
return func_hl
return async_func
@run_async
def is_db_updated(callback):
try:
util.database_check(db)
except:
callback(False)
callback(True)
@run_async
def is_bitcoin_updated(callback):
try:
util.bitcoind_check(db)
except:
callback(False)
callback(True)
@run_async
def is_version_updated(callback):
try:
util.versions_check()
except:
callback(False)
callback(True)
@run_async
def get_status(callback):
block_count_db, block_count_bitcoin = util.get_status(db)
callback((block_count_db, block_count_bitcoin))
class HomeHandler(tornado.web.RequestHandler):
def get(self):
supply = util.devise(db, util.cha_supply(db), 'CHA', 'output')
self.render("index.html", supply = supply)
class FreebiesHandler(tornado.web.RequestHandler):
def get(self):
self.render("freebies.html")
class TechnicalHandler(tornado.web.RequestHandler):
def get(self):
max_profit = config.MAX_PROFIT
house_edge = config.HOUSE_EDGE
burn_start = config.BURN_START
burn_end = config.BURN_END
unspendable = config.UNSPENDABLE
max_burn = config.MAX_BURN
multiplier = config.MULTIPLIER
multiplier_initial = config.MULTIPLIER_INITIAL
self.render("technical.html", max_profit = max_profit, house_edge = house_edge, burn_start = burn_start, burn_end = burn_end, unspendable = unspendable, max_burn = max_burn, multiplier = multiplier, multiplier_initial = multiplier_initial)
class ErrorHandler(tornado.web.RequestHandler):
def get(self):
global is_bitcoind_connected
error = 'An unknown error has occurred.'
info = None
if config.HAS_CONFIG==False:
error = 'You need to set up a Chancecoin config file at '+config.CONFIG_PATH+'. You can find an example config file <a href="https://raw2.github.com/chancecoin/chancecoin/master/example.conf">here</a>.'
if is_bitcoind_connected==False:
error = 'Cannot connect to Bitcoin. Please make sure you have bitcoind or Bitcoin-QT running and that your config file is set correctly at ' + config.CONFIG_PATH + '.'
self.render("error.html", error = error, info = info)
class ParticipateHandler(tornado.web.RequestHandler):
def get(self):
max_profit = config.MAX_PROFIT
house_edge = config.HOUSE_EDGE
burn_start = config.BURN_START
burn_end = config.BURN_END
unspendable = config.UNSPENDABLE
max_burn = config.MAX_BURN
multiplier = config.MULTIPLIER
multiplier_initial = config.MULTIPLIER_INITIAL
version = config.CLIENT_VERSION
self.render("participate.html", max_profit = max_profit, house_edge = house_edge, burn_start = burn_start, burn_end = burn_end, unspendable = unspendable, max_burn = max_burn, multiplier = multiplier, multiplier_initial = multiplier_initial, version = version)
class BalancesHandler(tornado.web.RequestHandler):
@tornado.web.asynchronous
@tornado.gen.coroutine
def get(self):
db_updated = yield tornado.gen.Task(is_db_updated)
bitcoin_updated = yield tornado.gen.Task(is_bitcoin_updated)
version_updated = yield tornado.gen.Task(is_version_updated)
block_count_db, block_count_bitcoin = yield tornado.gen.Task(get_status)
info = None
error = None
balances = util.get_balances(db, asset = 'CHA', order_by = 'amount', order_dir='desc')
balances = balance_tuples(balances)
self.render("balances.html", db_updated = db_updated, bitcoin_updated = bitcoin_updated, version_updated = version_updated, balances = balances, info = info, error = error, block_count_db = block_count_db, block_count_bitcoin = block_count_bitcoin)
class CasinoHandler(tornado.web.RequestHandler):
@tornado.web.asynchronous
@tornado.gen.coroutine
def get(self):
db_updated = yield tornado.gen.Task(is_db_updated)
bitcoin_updated = yield tornado.gen.Task(is_bitcoin_updated)
version_updated = yield tornado.gen.Task(is_version_updated)
block_count_db, block_count_bitcoin = yield tornado.gen.Task(get_status)
info = None
error = None
bets = util.get_bets(db, order_by='tx_index', validity='valid')
bets = bet_tuples(bets[:100])
my_bets = []
supply = util.devise(db, util.cha_supply(db), 'CHA', 'output')
max_profit = float(supply)*config.MAX_PROFIT
self.render("casino.html", db_updated = db_updated, bitcoin_updated = bitcoin_updated, version_updated = version_updated, bets = bets, my_bets = my_bets, supply = supply, house_edge = config.HOUSE_EDGE, max_profit = max_profit, info = info, error = error, block_count_db = block_count_db, block_count_bitcoin = block_count_bitcoin)
@tornado.web.asynchronous
@tornado.gen.coroutine
def post(self):
db_updated = yield tornado.gen.Task(is_db_updated)
bitcoin_updated = yield tornado.gen.Task(is_bitcoin_updated)
version_updated = yield tornado.gen.Task(is_version_updated)
block_count_db, block_count_bitcoin = yield tornado.gen.Task(get_status)
info = None
error = None
bets = util.get_bets(db, order_by='tx_index', validity='valid')
bets = bet_tuples(bets[:100])
my_bets = []
supply = util.devise(db, util.cha_supply(db), 'CHA', 'output')
max_profit = float(supply)*config.MAX_PROFIT
if self.get_argument("form")=="roll" and self.get_argument("source") and self.get_argument("bet") and self.get_argument("payout") and self.get_argument("chance"):
source = self.get_argument("source")
bet_amount = util.devise(db, self.get_argument("bet"), 'CHA', 'input')
chance = util.devise(db, self.get_argument("chance"), 'value', 'input')
payout = util.devise(db, self.get_argument("payout"), 'value', 'input')
try:
tx_hex = bet.create(db, source, bet_amount, chance, payout, unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "Thanks for betting!"
except:
error = sys.exc_info()[1]
elif self.get_argument("form")=="my_bets" and self.get_argument("address"):
try:
my_bets = util.get_bets(db, source = self.get_argument("address"), order_by='tx_index', validity='valid')
my_bets = bet_tuples(my_bets)
except:
my_bets = []
self.render("casino.html", db_updated = db_updated, bitcoin_updated = bitcoin_updated, version_updated = version_updated, bets = bets, my_bets = my_bets, supply = supply, house_edge = config.HOUSE_EDGE, max_profit = max_profit, info = info, error = error, block_count_db = block_count_db, block_count_bitcoin = block_count_bitcoin)
class WalletHandler(tornado.web.RequestHandler):
@tornado.web.asynchronous
@tornado.gen.coroutine
def get(self):
db_updated = yield tornado.gen.Task(is_db_updated)
bitcoin_updated = yield tornado.gen.Task(is_bitcoin_updated)
version_updated = yield tornado.gen.Task(is_version_updated)
block_count_db, block_count_bitcoin = yield tornado.gen.Task(get_status)
info = None
error = None
orders_sell = util.get_orders(db, validity='valid', show_empty=False, show_expired=False, filters=[{'field': 'give_asset', 'op': '==', 'value': 'CHA'},{'field': 'get_asset', 'op': '==', 'value': 'BTC'}])
orders_buy = util.get_orders(db, validity='valid', show_empty=False, show_expired=False, filters=[{'field': 'get_asset', 'op': '==', 'value': 'CHA'},{'field': 'give_asset', 'op': '==', 'value': 'BTC'}])
orders_sell = sorted(order_tuples(orders_sell), key=lambda tup: tup[1], reverse=True)
orders_buy = sorted(order_tuples(orders_buy), key=lambda tup: tup[1], reverse=True)
my_orders = None
my_order_matches = None
balance = None
self.render("wallet.html", db_updated = db_updated, bitcoin_updated = bitcoin_updated, version_updated = version_updated, wallet = None, orders_buy = orders_buy, orders_sell = orders_sell, info = info, error = error, block_count_db = block_count_db, block_count_bitcoin = block_count_bitcoin, balance = balance, my_orders = my_orders, my_order_matches = my_order_matches)
@tornado.web.asynchronous
@tornado.gen.coroutine
def post(self):
db_updated = yield tornado.gen.Task(is_db_updated)
bitcoin_updated = yield tornado.gen.Task(is_bitcoin_updated)
version_updated = yield tornado.gen.Task(is_version_updated)
block_count_db, block_count_bitcoin = yield tornado.gen.Task(get_status)
info = None
error = None
orders_sell = util.get_orders(db, validity='valid', show_empty=False, show_expired=False, filters=[{'field': 'give_asset', 'op': '==', 'value': 'CHA'},{'field': 'get_asset', 'op': '==', 'value': 'BTC'}])
orders_buy = util.get_orders(db, validity='valid', show_empty=False, show_expired=False, filters=[{'field': 'get_asset', 'op': '==', 'value': 'CHA'},{'field': 'give_asset', 'op': '==', 'value': 'BTC'}])
orders_sell = sorted(order_tuples(orders_sell), key=lambda tup: tup[1], reverse=True)
orders_buy = sorted(order_tuples(orders_buy), key=lambda tup: tup[1], reverse=True)
my_orders = None
my_order_matches = None
balance = None
if self.get_argument("form")=="balance":
address = self.get_argument("address")
try:
wallet = util.get_address(db, address = address)
except:
wallet = None
balance = None
if wallet != None:
for balance in wallet['balances']:
if balance['asset']=='CHA':
balance = util.devise(db, balance['amount'], 'CHA', 'output')
elif self.get_argument("form")=="my_orders":
address = self.get_argument("address")
try:
my_orders = util.get_orders(db, validity='valid', show_empty=False, show_expired=False, source=address)
my_orders = order_tuples(my_orders)
my_order_matches = util.get_order_matches(db, validity='pending', is_mine=True, address=address)
my_order_matches = order_match_tuples(my_order_matches)
except:
my_orders = None
my_order_matches = None
elif self.get_argument("form")=="btcpay":
order_match_id = self.get_argument("order_match_id")
try:
tx_hex = btcpay.create(db, order_match_id, unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "BTC payment successful"
except:
error = sys.exc_info()[1]
elif self.get_argument("form")=="cancel":
tx_hash = self.get_argument("tx_hash")
try:
tx_hex = cancel.create(db, tx_hash, unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "Cancel successful"
except:
error = sys.exc_info()[1]
elif self.get_argument("form")=="send":
source = self.get_argument("source")
destination = self.get_argument("destination")
quantity = util.devise(db, self.get_argument("quantity"), 'CHA', 'input')
try:
tx_hex = send.create(db, source, destination, quantity, 'CHA', unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "Send successful"
except:
error = sys.exc_info()[1]
elif self.get_argument("form")=="burn":
source = self.get_argument("source")
quantity = util.devise(db, self.get_argument("quantity"), 'CHA', 'input')
try:
tx_hex = burn.create(db, source, quantity, unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "Burn successful"
except:
error = sys.exc_info()[1]
elif self.get_argument("form")=="buy":
source = self.get_argument("source")
quantity = util.devise(db, self.get_argument("quantity"), 'CHA', 'input')
price = util.devise(db, self.get_argument("price"), 'value', 'input')
pricetimesquantity = float(self.get_argument("quantity"))*float(self.get_argument("price"))
pricetimesquantity = int(pricetimesquantity*config.UNIT)
expiration = 6 * 24 #24 hour order
try:
tx_hex = order.create(db, source, 'BTC', pricetimesquantity, 'CHA', quantity,
expiration, 0, config.MIN_FEE, unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "Buy order successful"
except:
error = sys.exc_info()[1]
elif self.get_argument("form")=="sell":
source = self.get_argument("source")
quantity = util.devise(db, self.get_argument("quantity"), 'CHA', 'input')
price = util.devise(db, self.get_argument("price"), 'value', 'input')
pricetimesquantity = float(self.get_argument("quantity"))*float(self.get_argument("price"))
pricetimesquantity = int(pricetimesquantity*config.UNIT)
expiration = 6 * 24 #24 hour order
try:
tx_hex = order.create(db, source, 'CHA', quantity, 'BTC', pricetimesquantity,
expiration, 0, config.MIN_FEE, unsigned=False)
bitcoin.transmit(tx_hex, ask=False)
info = "Sell order successful"
except:
error = sys.exc_info()[1]
self.render("wallet.html", db_updated = db_updated, bitcoin_updated = bitcoin_updated, version_updated = version_updated, orders_buy = orders_buy, orders_sell = orders_sell, info = info, error = error, block_count_db = block_count_db, block_count_bitcoin = block_count_bitcoin, balance = balance, my_orders = my_orders, my_order_matches = my_order_matches)
class Application(tornado.web.Application):
def __init__(self):
global is_bitcoind_connected
is_bitcoind_connected = util.is_bitcoind_connected()
if db==None or is_bitcoind_connected == False:
handlers = [
(r"/", ErrorHandler),
(r"/wallet", ErrorHandler),
(r"/casino", ErrorHandler),
(r"/balances", ErrorHandler),
(r"/participate", ErrorHandler),
(r"/technical", ErrorHandler),
(r"/freebies", ErrorHandler),
]
else:
handlers = [
(r"/", HomeHandler),
(r"/wallet", WalletHandler),
(r"/casino", CasinoHandler),
(r"/balances", BalancesHandler),
(r"/participate", ParticipateHandler),
(r"/technical", TechnicalHandler),
(r"/freebies", FreebiesHandler),
]
if getattr(sys, 'frozen', False):
file_frozen = sys.executable
else:
file_frozen = __file__
settings = dict(
template_path=os.path.join(os.path.dirname(file_frozen), "templates"),
static_path=os.path.join(os.path.dirname(file_frozen), "static"),
debug=True
)
tornado.web.Application.__init__(self, handlers, **settings)
def start():
http_server = tornado.httpserver.HTTPServer(Application())
http_server.listen(8080)
tornado.ioloop.IOLoop.instance().start()
if __name__ == "__main__":
start()
|
chancecoin/chancecoin
|
server.py
|
Python
|
mit
| 18,659
|
[
"CASINO"
] |
d182eab6fc021407f6d9735e61ac0fd1ecbad8c4ff18fbb963aa478595e6c6c7
|
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_base.form.old_forms import BaseModelForm
from edc_constants.constants import ON_STUDY
from edc_visit_tracking.forms import VisitFormMixin
from tshilo_dikotla.choices import VISIT_REASON, VISIT_INFO_SOURCE, INFANT_VISIT_STUDY_STATUS, INFO_PROVIDER
from td_maternal.models import MaternalConsent, MaternalDeathReport, TdConsentVersion
from ..models import InfantVisit
from td_maternal.models.maternal_eligibility import MaternalEligibility
class InfantVisitForm(VisitFormMixin, BaseModelForm):
participant_label = 'infant'
information_provider = forms.ChoiceField(
label='Please indicate who provided most of the information for this infant\'s visit',
choices=INFO_PROVIDER,
initial='MOTHER',
widget=AdminRadioSelect(renderer=AdminRadioFieldRenderer))
study_status = forms.ChoiceField(
label='What is the infant\'s current study status',
choices=INFANT_VISIT_STUDY_STATUS,
initial=ON_STUDY,
widget=AdminRadioSelect(renderer=AdminRadioFieldRenderer))
reason = forms.ChoiceField(
label='Reason for visit',
choices=[choice for choice in VISIT_REASON],
widget=AdminRadioSelect(renderer=AdminRadioFieldRenderer))
info_source = forms.ChoiceField(
required=False,
label='Source of information',
choices=[choice for choice in VISIT_INFO_SOURCE],
widget=AdminRadioSelect(renderer=AdminRadioFieldRenderer))
def clean(self):
cleaned_data = super(InfantVisitForm, self).clean()
self.validate_current_consent_version()
# self.validate_reason_visit_missed()
# self.validate_report_datetime_and_consent()
# self.validate_information_provider_is_alive()
return cleaned_data
def validate_report_datetime_and_consent(self):
cleaned_data = self.cleaned_data
try:
relative_identifier = cleaned_data.get(
'appointment').registered_subject.relative_identifier
maternal_consent = MaternalConsent.objects.filter(
registered_subject__subject_identifier=relative_identifier).order_by('consent_datetime').last()
if cleaned_data.get("report_datetime") < maternal_consent.consent_datetime:
raise forms.ValidationError(
"Report datetime cannot be before consent datetime")
if cleaned_data.get("report_datetime").date() < maternal_consent.dob:
raise forms.ValidationError(
"Report datetime cannot be before DOB")
except MaternalConsent.DoesNotExist:
raise forms.ValidationError('Maternal consent does not exist.')
def validate_information_provider_is_alive(self):
cleaned_data = self.cleaned_data
try:
if cleaned_data.get('information_provider') == 'MOTHER':
relative_identifier = cleaned_data.get(
'appointment').registered_subject.relative_identifier
maternal_death_report = MaternalDeathReport.objects.get(
maternal_visit__appointment__registered_subject__subject_identifier=relative_identifier,
death_date__lte=cleaned_data.get("report_datetime").date())
raise forms.ValidationError(
'The mother was reported deceased on {}.'
'The information provider cannot be the \'mother\'.'.format(
maternal_death_report.death_date.strftime('%Y-%m-%d')))
except MaternalDeathReport.DoesNotExist:
pass
def validate_current_consent_version(self):
try:
td_consent_version = TdConsentVersion.objects.get(
maternal_eligibility=self.maternal_eligibility)
except TdConsentVersion.DoesNotExist:
raise forms.ValidationError(
'Complete mother\'s consent version form before proceeding')
else:
try:
MaternalConsent.objects.get(
maternal_eligibility=self.maternal_eligibility,
version=td_consent_version.version)
except MaternalConsent.DoesNotExist:
raise forms.ValidationError(
'Maternal Consent form for version {} before proceeding'.format(td_consent_version.version))
@property
def maternal_eligibility(self):
cleaned_data = self.cleaned_data
relative_identifier = cleaned_data.get(
'appointment').registered_subject.relative_identifier
try:
return MaternalEligibility.objects.get(
registered_subject__subject_identifier=relative_identifier)
except MaternalEligibility.DoesNotExist:
pass
class Meta:
model = InfantVisit
fields = '__all__'
|
botswana-harvard/tshilo-dikotla
|
td_infant/forms/infant_visit_form.py
|
Python
|
gpl-2.0
| 4,943
|
[
"VisIt"
] |
8ba640934f29985b31b664e96ad7f86cd2284c5836474923e8b12e1fd626b038
|
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
from __future__ import annotations
from typing import Union
import os
import logging
from os import remove
from os import rename
from shutil import copyfile
from copy import copy
from kivy.logger import Logger
from ORCA.utils.LogError import LogError
from ORCA.vars.Replace import ReplaceVars
from ORCA.utils.Path import cPath
from ORCA.utils.Path import CleanUp
from ORCA.utils.TypeConvert import ToUnicode
from os.path import basename
from os.path import isfile
from ORCA.utils.Path import AdjustPathToUnix
uSeparator = os.sep
__all__ = ["cFileName"]
class cFileName:
def __init__(self,uFile: Union[str,cPath,cFileName] = u''):
self.oPath: cPath = cPath()
self.uRaw: str
if isinstance(uFile, str):
self.uRaw = uFile
elif isinstance(uFile, cPath):
self.oPath = uFile
self.uRaw = u''
elif isinstance(uFile, cFileName):
self.oPath = uFile.oPath
self.uRaw = uFile.uRaw
else:
LogError(uMsg="cFileName, illegal constructor:"+str(type(uFile)))
self.uFinal: str = u''
self.bDirty: bool = True
if Logger.level==logging.DEBUG and False:
if self.uRaw:
for uChar in u"/\\:":
if uChar in self.uRaw:
LogError(uMsg="do not pass full strings to a filename (use import):"+str(uFile), bTrackStack=True)
def __str__(self) ->str:
if not self.bDirty:
return self.uFinal
else:
self._CreateFinal()
return self.uFinal
def __add__(self, uFile: str) ->cFileName:
if isinstance(uFile, str):
oRet: cFileName = copy(self)
oRet.uRaw += uFile
oRet.bDirty = True
if Logger.level ==logging.DEBUG:
for uChar in u"/\\:":
if uChar in self.uRaw:
LogError(uMsg="do not pass full strings to a filename (use import)", bTrackStack=True)
return oRet
else:
LogError(uMsg="cFileName, illegal add:"+str(type(uFile)))
return self
def __radd__(self, uOther: str) ->str:
if isinstance(uOther, str):
return uOther+self.string
else:
return uOther
@property
def basename(self) ->str:
return self.uRaw
@property
def string(self) ->str:
if not self.bDirty:
return self.uFinal
else:
self._CreateFinal()
return self.uFinal
@property
def unixstring(self) ->str:
return AdjustPathToUnix(uPath=self.string)
@property
def urlstring(self) ->str:
return AdjustPathToUnix(uPath=self.string).replace(":/", "://")
def _CreateFinal(self) ->None:
self.bDirty = False
if self.uRaw:
self.uFinal = CleanUp(uFinal=ReplaceVars(self.oPath.uRaw)+ ReplaceVars(self.uRaw))
else:
self.uFinal=u''
def Clear(self) ->cFileName:
self.oPath.uRaw = u''
self.uRaw = u''
self.bDirty = True
return self
def Exists(self) ->bool:
"""
Checks, if a file exists
:return: Returns True if the the given filename exists
"""
return isfile(self.string)
def Copy(self,*,oNewFile: Union[cFileName,cPath]) ->bool:
"""
Copies a file
:param cFileName/cPath oNewFile: Destination file name or destination path
:return: True, if successful
"""
try:
if isinstance(oNewFile,cFileName):
copyfile(self.string,oNewFile.string)
else:
oNewFileTmp=cFileName(oNewFile)+self.basename
copyfile(self.string, oNewFileTmp.string)
return True
except Exception as e:
LogError (uMsg=u'can\'t copy file [%s] to [%s]' % (self.string,oNewFile.string),oException=e)
return False
def ImportFullPath(self,*,uFnFullName: str) ->cFileName:
if uFnFullName.startswith("$var("):
if uFnFullName.endswith(")"):
if not uSeparator in uFnFullName:
Logger.warning("Variable on FileName needs to replaced on import, is this what you want?:"+uFnFullName)
uFnFullName = ReplaceVars(uFnFullName)
self.oPath.ImportFullPath(uFnFullName=uFnFullName)
self.uRaw=basename(uFnFullName)
self.bDirty = True
return self
def Delete(self) ->bool:
"""
Deletes a files
:return: True, if successful
"""
try:
remove(self.string)
return True
except Exception as e:
uMsg=u'can\'t delete File %s:%s' % (ToUnicode(e),self.string)
Logger.warning (uMsg)
return False
def Rename(self,*,oNewFileName: cFileName) ->bool:
"""
Renames a File
:param cFileName oNewFileName: New file name
:return: True, if successful
"""
try:
if self.Exists():
if not oNewFileName.Exists():
rename(self.string,oNewFileName.string)
return True
return False
except Exception as e:
LogError (uMsg=u'can\'t rename file [%s] to [%s]' % (self.string,oNewFileName.string),oException=e)
return False
def IsEmpty(self) ->bool:
"""
Returns, if the FileName object is empty
:return: True / False
"""
return self.uRaw==u''
def Size(self) ->int:
"""
Returns the size of a file
:return: File size of -1 on error
"""
try:
return os.path.getsize(self.string)
except Exception as e:
LogError (uMsg=u'can\'t get filesize [%s]' % self.string, oException=e)
return -1
def Extension(self) -> str:
"""
Returns the extension of a file (with dot)
:return: extension as str
"""
try:
return os.path.splitext(self.string)[1]
except Exception as e:
LogError (uMsg=u'can\'t get file extension [%s]' % self.string, oException=e)
return ""
|
thica/ORCA-Remote
|
src/ORCA/utils/FileName.py
|
Python
|
gpl-3.0
| 7,486
|
[
"ORCA"
] |
259f777ac8599dfc8857ba3ae4f7793a5d0ece9760c69a4b0d534d55e5d7a3c6
|
TEX = """
text here \citet{robitaille:08:2413}
more \cite{forbrich:10:1453} text
(\citealt{robitaille:06:256})
"""
EXPECTED = r"""
@ARTICLE{forbrich:10:1453,
author = {{Forbrich}, J. and {Tappe}, A. and {Robitaille}, T. and {Muench}, A.~A. and
{Teixeira}, P.~S. and {Lada}, E.~A. and {Stolte}, A. and {Lada}, C.~J.
},
title = "{Disentangling Protostellar Evolutionary Stages in Clustered Environments Using Spitzer-IRS Spectra and Comprehensive Spectral Energy Distribution Modeling}",
journal = {\apj},
archivePrefix = "arXiv",
primaryClass = "astro-ph.SR",
keywords = {circumstellar matter, infrared: stars, open clusters and associations: individual: NGC 2264 IC 348},
year = 2010,
month = jun,
volume = 716,
pages = {1453-1477},
doi = {10.1088/0004-637X/716/2/1453},
adsurl = {http://adsabs.harvard.edu/abs/2010ApJ...716.1453F},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@ARTICLE{robitaille:06:256,
author = {{Robitaille}, T.~P. and {Whitney}, B.~A. and {Indebetouw}, R. and
{Wood}, K. and {Denzmore}, P.},
title = "{Interpreting Spectral Energy Distributions from Young Stellar Objects. I. A Grid of 200,000 YSO Model SEDs}",
journal = {\apjs},
keywords = {Astronomical Data Bases: Miscellaneous, Stars: Circumstellar Matter, Infrared: Stars, Polarization, Radiative Transfer, Stars: Formation, Stars: Pre-Main-Sequence},
year = 2006,
month = dec,
volume = 167,
pages = {256-285},
doi = {10.1086/508424},
adsurl = {http://adsabs.harvard.edu/abs/2006ApJS..167..256R},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@ARTICLE{robitaille:08:2413,
author = {{Robitaille}, T.~P. and {Meade}, M.~R. and {Babler}, B.~L. and
{Whitney}, B.~A. and {Johnston}, K.~G. and {Indebetouw}, R. and
{Cohen}, M. and {Povich}, M.~S. and {Sewilo}, M. and {Benjamin}, R.~A. and
{Churchwell}, E.},
title = "{Intrinsically Red Sources Observed by Spitzer in the Galactic Midplane}",
journal = {\aj},
archivePrefix = "arXiv",
keywords = {catalogs, infrared: stars, Galaxy: stellar content, planetary nebulae: general, stars: AGB and post-AGB, stars: formation},
year = 2008,
month = dec,
volume = 136,
pages = {2413-2440},
doi = {10.1088/0004-6256/136/6/2413},
adsurl = {http://adsabs.harvard.edu/abs/2008AJ....136.2413R},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
"""
from auto_bibtex import main
def test_main(tmpdir):
filename = tmpdir.join('ms.tex').strpath
with open(filename, 'w') as f:
f.write(TEX)
output = main(filename)
assert output.strip() == EXPECTED.strip()
|
astrofrog/auto_bibtex
|
test_auto_bibtex.py
|
Python
|
mit
| 2,663
|
[
"Galaxy"
] |
286c4cb3d5ef50b1eb6cc6f9acff4b1d2d3d0526c14a5aff61659cc213dca686
|
from __future__ import absolute_import
from django.utils.translation import ugettext_lazy as _
from sentry import http, options
from sentry.identity.pipeline import IdentityProviderPipeline
from sentry.identity.github import get_user_info
from sentry.integrations import Integration, IntegrationFeatures, IntegrationProvider, IntegrationMetadata
from sentry.integrations.exceptions import ApiError
from sentry.integrations.constants import ERR_INTERNAL, ERR_UNAUTHORIZED
from sentry.integrations.repositories import RepositoryMixin
from sentry.pipeline import NestedPipelineView, PipelineView
from sentry.utils.http import absolute_uri
from .client import GitHubAppsClient
from .issues import GitHubIssueBasic
from .repository import GitHubRepositoryProvider
from .utils import get_jwt
DESCRIPTION = """
Define a relationship between Sentry and GitHub.
* Authorize repositories to be added for syncing commit data.
* Create or link existing GitHub issues. (coming soon)
"""
disable_dialog = {
'actionText': 'Visit GitHub',
'body': 'Before deleting this integration, you must uninstall this integration from GitHub. After uninstalling, your integration will be disabled at which point you can choose to delete this integration.'
}
removal_dialog = {
'actionText': 'Delete',
'body': 'Deleting this integration will delete all associated repositories and commit data. This action cannot be undone. Are you sure you want to delete your integration?'
}
metadata = IntegrationMetadata(
description=DESCRIPTION.strip(),
author='The Sentry Team',
noun=_('Installation'),
issue_url='https://github.com/getsentry/sentry/issues/new?title=GitHub%20Integration:%20&labels=Component%3A%20Integrations',
source_url='https://github.com/getsentry/sentry/tree/master/src/sentry/integrations/github',
aspects={
'disable_dialog': disable_dialog,
'removal_dialog': removal_dialog,
},
)
API_ERRORS = {
404: 'GitHub returned a 404 Not Found error. If this repository exists, ensure'
' that your installation has permission to access this repository'
' (https://github.com/settings/installations).',
401: ERR_UNAUTHORIZED,
}
class GitHubIntegration(Integration, GitHubIssueBasic, RepositoryMixin):
def get_client(self):
return GitHubAppsClient(integration=self.model)
def get_repositories(self):
return self.get_client().get_repositories()
def reinstall(self):
self.reinstall_repositories()
def message_from_error(self, exc):
if isinstance(exc, ApiError):
message = API_ERRORS.get(exc.code)
if message:
return message
return (
'Error Communicating with GitHub (HTTP %s): %s' % (
exc.code, exc.json.get('message', 'unknown error')
if exc.json else 'unknown error',
)
)
else:
return ERR_INTERNAL
class GitHubIntegrationProvider(IntegrationProvider):
key = 'github'
name = 'GitHub'
metadata = metadata
integration_cls = GitHubIntegration
features = frozenset([
IntegrationFeatures.COMMITS,
IntegrationFeatures.ISSUE_BASIC,
])
setup_dialog_config = {
'width': 1030,
'height': 1000,
}
def get_pipeline_views(self):
identity_pipeline_config = {
'oauth_scopes': (),
'redirect_url': absolute_uri('/extensions/github/setup/'),
}
identity_pipeline_view = NestedPipelineView(
bind_key='identity',
provider_key='github',
pipeline_cls=IdentityProviderPipeline,
config=identity_pipeline_config,
)
return [GitHubInstallationRedirect(), identity_pipeline_view]
def get_installation_info(self, access_token, installation_id):
session = http.build_session()
resp = session.get(
'https://api.github.com/app/installations/%s' % installation_id,
headers={
'Authorization': 'Bearer %s' % get_jwt(),
'Accept': 'application/vnd.github.machine-man-preview+json',
}
)
resp.raise_for_status()
installation_resp = resp.json()
resp = session.get(
'https://api.github.com/user/installations',
params={'access_token': access_token},
headers={'Accept': 'application/vnd.github.machine-man-preview+json'}
)
resp.raise_for_status()
user_installations_resp = resp.json()
# verify that user actually has access to the installation
for installation in user_installations_resp['installations']:
if installation['id'] == installation_resp['id']:
return installation_resp
return None
def build_integration(self, state):
identity = state['identity']['data']
user = get_user_info(identity['access_token'])
installation = self.get_installation_info(
identity['access_token'], state['installation_id'])
integration = {
'name': installation['account']['login'],
# TODO(adhiraj): This should be a constant representing the entire github cloud.
'external_id': installation['id'],
# GitHub identity is associated directly to the application, *not*
# to the installation itself.
'idp_external_id': installation['app_id'],
'metadata': {
# The access token will be populated upon API usage
'access_token': None,
'expires_at': None,
'icon': installation['account']['avatar_url'],
'domain_name': installation['account']['html_url'].replace('https://', ''),
'account_type': installation['account']['type'],
},
'user_identity': {
'type': 'github',
'external_id': user['id'],
'scopes': [], # GitHub apps do not have user scopes
'data': {'access_token': identity['access_token']},
},
}
if state.get('reinstall_id'):
integration['reinstall_id'] = state['reinstall_id']
return integration
def setup(self):
from sentry.plugins import bindings
bindings.add(
'integration-repository.provider',
GitHubRepositoryProvider,
id='integrations:github',
)
class GitHubInstallationRedirect(PipelineView):
def get_app_url(self):
name = options.get('github-app.name')
return 'https://github.com/apps/%s' % name
def dispatch(self, request, pipeline):
if 'reinstall_id' in request.GET:
pipeline.bind_state('reinstall_id', request.GET['reinstall_id'])
if 'installation_id' in request.GET:
pipeline.bind_state('installation_id', request.GET['installation_id'])
return pipeline.next_step()
return self.redirect(self.get_app_url())
|
looker/sentry
|
src/sentry/integrations/github/integration.py
|
Python
|
bsd-3-clause
| 7,082
|
[
"VisIt"
] |
1795a0ce0a2d94a27b4dddf4fb461dc7d64432a0aa4dfd0a82792d083e87e546
|
# PrequelPrizes server-side code Copyright (c) 2013 Chris Cogdon - chris@cogdon.org
import codecs
import csv
from uuid import uuid4
import hmac
import hashlib
import sys
import cStringIO
from django import forms
from django.contrib.auth.decorators import permission_required
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.http import QueryDict
from django.shortcuts import render, redirect, HttpResponse
from django.utils.timezone import now
from django.conf import settings
from django.views.decorators.cache import never_cache, cache_control
from models import Winner
PRIZES_SECRET_KEY_STR = settings.PRIZES_SECRET_KEY.decode("hex")
@never_cache
def get_key(request):
count = Winner.objects.exclude(details_time=None).values("authentication_ip").distinct().count()
if count >= settings.PRIZES_NUM_PRIZES:
return HttpResponse("0", mimetype="text/plain")
else:
u4 = uuid4()
return HttpResponse(u4.hex, mimetype="text/plain")
class PrizesError(PermissionDenied):
pass
@never_cache
def check_key(request):
key = request.REQUEST.get("key")
time = request.REQUEST.get("time")
sign = request.REQUEST.get("sign")
if key is None or sign is None or time is None:
raise PrizesError("There seems to be a bunch of information missing from that URL. "
"You're not supposed to visit it directly, you know.")
cc = request.REQUEST.get("cc")
h1 = hmac.new(PRIZES_SECRET_KEY_STR, key + time, hashlib.sha1)
if len(key) != 32 or h1.hexdigest() != sign:
raise PrizesError("I'm pretty sure the game did not generate those numbers. "
"Are you up to... shenanigans?")
try:
game_time = float(time)
except ValueError:
raise PrizesError("That doesn't look like a valid game time. I think we messed up here.")
try:
winner = Winner.objects.get(key=key)
except Winner.DoesNotExist:
if settings.PRIZES_DISABLED:
raise PrizesError("Somehow you managed to get the game to generate a prize link long after "
"all the prizes have been collected. Congratulations on doing that part, "
"but still no prize. Sorry.")
winner = Winner(key=key, creation_ip=request.META.get("REMOTE_ADDR"))
winner.authentication_time = now()
winner.authentication_ip = request.META.get("REMOTE_ADDR")
winner.game_time = game_time
winner.save()
if cc == "yep":
if request.session.test_cookie_worked():
request.session['authenticated_winner'] = winner.id
request.session.delete_test_cookie()
return redirect(enter_details)
else:
return render(request, "prizes/no_cookies.html", {"key": key, "time": time, "sign": sign})
else:
request.session.set_test_cookie()
qd = QueryDict('', mutable=True)
qd.update({"key": key, "time": time, "sign": sign, "cc": "yep"})
return redirect(reverse(check_key) + "?" + qd.urlencode())
def get_winner(request):
winner_id = request.session.get('authenticated_winner')
if winner_id is None:
raise PrizesError(
"You have not been authenticated yet. "
"Cookies blocked after I spent all that effort checking them for you? "
"Bypassed the checkkey page by being sneaky?")
try:
winner = Winner.objects.get(id=winner_id)
except Winner.DoesNotExist:
raise PrizesError("The authenticated winner doesn't exist. How did you manage that? Amazing!")
return winner
class WinnerForm(forms.ModelForm):
email = forms.EmailField(max_length=80, widget=forms.TextInput(attrs={"size": "40"}))
name = forms.CharField(max_length=80, widget=forms.TextInput(attrs={"size": "40"}))
address1 = forms.CharField(max_length=80, widget=forms.TextInput(attrs={"size": "40"}), label="Address")
address2 = forms.CharField(max_length=80, required=False, widget=forms.TextInput(attrs={"size": "40"}), label="")
city = forms.CharField(max_length=80, widget=forms.TextInput(attrs={"size": "40"}))
state = forms.CharField(max_length=80, required=False, widget=forms.TextInput(attrs={"size": "40"}))
postcode = forms.CharField(max_length=80, widget=forms.TextInput(attrs={"size": "40"}), label="ZIP/Postcode")
country = forms.CharField(max_length=80, required=False, widget=forms.TextInput(attrs={"size": "40"}))
class Meta:
model = Winner
fields = ["email", "name", "address1", "address2", "city", "state", "postcode", "country"]
@cache_control(private=True)
def enter_details(request):
winner = get_winner(request)
if request.method == "POST":
form = WinnerForm(request.POST, instance=winner)
if form.is_valid():
winner = form.save(commit=False)
winner.details_time = now()
winner.details_ip = request.META.get("REMOTE_ADDR")
winner.save()
return redirect(thanks)
else:
form = WinnerForm(instance=winner)
return render(request, "prizes/enter_details.html", {"form": form, "winner": winner})
@cache_control(private=True)
def thanks(request):
try:
winner = get_winner(request)
except PrizesError:
winner = None
request.session.pop('authenticated_winner', None)
return render(request, "prizes/thanks.html", {"winner": winner})
def handler403(request):
exc_value = sys.exc_info()[1]
exc_message = str(exc_value)
return render(request, "403.html", {"exc_message": exc_message})
class UnicodeCSVWriter:
"""
A CSV writer which will write rows to CSV file "f",
which is encoded in the given encoding.
"""
def __init__(self, f, dialect=csv.excel, encoding="utf-8", **kwds):
# Redirect output to a queue
self.queue = cStringIO.StringIO()
self.writer = csv.writer(self.queue, dialect=dialect, **kwds)
self.stream = f
self.encoder = codecs.getincrementalencoder(encoding)()
def writerow(self, row):
self.writer.writerow([unicode(s).encode("utf-8") for s in row])
# Fetch UTF-8 output from the queue ...
data = self.queue.getvalue()
data = data.decode("utf-8")
# ... and reencode it into the target encoding
data = self.encoder.encode(data)
# write to the target stream
self.stream.write(data)
# empty queue
self.queue.truncate(0)
def writerows(self, rows):
for row in rows:
self.writerow(row)
@permission_required('prizes.change_winner')
def csv_dump(request):
response = HttpResponse(mimetype="text/csv")
response['Content-Disposition'] = 'attachment; filename="winners.csv"'
outp = UnicodeCSVWriter(response)
outp.writerow(('email', 'name', 'address1', 'address2', 'city', 'state', 'postcode', 'country'))
for w in Winner.objects.exclude(details_time=None):
outp.writerow((w.email, w.name, w.address1, w.address2, w.city, w.state, w.postcode, w.country))
return response
|
chmarr/prequelprizes
|
prizes/views.py
|
Python
|
gpl-2.0
| 7,156
|
[
"VisIt"
] |
e38f46c3bb9f48f4e7ce8527e05334f35449c188848539262fdc3b1b503213bb
|
# Python Imports
import datetime
# Rest Framework Imports
from rest_framework import serializers
from rest_framework import viewsets
from rest_framework.decorators import detail_route, list_route
from rest_framework.response import Response
#Local Imports
import contacts.models as cont
from messages import ParticipantSimpleSerializer
import utils
class VisitSerializer(serializers.ModelSerializer):
href = serializers.HyperlinkedIdentityField(view_name='visit-detail')
participant = ParticipantSimpleSerializer()
status = serializers.SerializerMethodField()
days_str = serializers.CharField()
is_pregnant = serializers.BooleanField(read_only=True)
visit_type_display = serializers.CharField(source='get_visit_type_display')
class Meta:
model = cont.Visit
fields = ('id','href','participant','scheduled','arrived','notification_last_seen','status',
'comment','visit_type','visit_type_display','days_overdue','days_str','is_pregnant')
def get_status(self,obj):
return obj.get_status_display()
class VisitSimpleSerializer(serializers.ModelSerializer):
href = serializers.HyperlinkedIdentityField(view_name='visit-detail')
status = serializers.SerializerMethodField()
days_str = serializers.CharField()
visit_type_display = serializers.CharField(source='get_visit_type_display')
class Meta:
model = cont.Visit
fields = ('id','href','scheduled','arrived','notification_last_seen','status',
'comment','visit_type','visit_type_display','days_overdue','days_str')
def get_status(self,obj):
return obj.get_status_display()
class VisitViewSet(viewsets.ModelViewSet):
queryset = cont.Visit.objects.all()
serializer_class = VisitSerializer
@list_route()
def upcoming(self, request):
queryset = self.queryset.for_user(request.user).visit_range(start={'days':-14},end={'days':0}).order_by('scheduled')
serializer = self.get_serializer(queryset, many=True)
return Response(serializer.data)
@detail_route(methods=['put'])
def seen(self, request, pk):
instance = self.get_object()
instance.seen()
cont.EventLog.objects.create(user=request.user,event='visit.seen',data={'visit_id':instance.id})
visit = VisitSerializer(instance,context={'request':request})
return Response(visit.data)
@detail_route(methods=['put'])
def attended(self, request, pk):
instance = self.get_object()
instance.attended(request.data.get('arrived',None))
instance_serialized = VisitSerializer(instance,context={'request':request}).data
# Make next visit if needed
next_visit_serialized = None
if request.data.has_key('next'):
# print 'Next Visit',request.data['next']
next_visit = instance.participant.visit_set.create(
scheduled=utils.angular_datepicker(request.data['next']),
visit_type=request.data['type']
)
next_visit_serialized = VisitSerializer(next_visit,context={'request':request}).data
# send visit attended reminder
instance.send_visit_attended_message()
cont.EventLog.objects.create(user=request.user,event='visit.attended',data={'visit_id':instance.id})
return Response({'visit':instance_serialized,'next':next_visit_serialized})
@detail_route(methods=['put'])
def missed(self, request, pk):
instance = self.get_object()
instance.set_status('missed')
instance_serialized = VisitSerializer(instance,context={'request':request}).data
return Response(instance_serialized)
@detail_route(methods=['put'])
def edit(self, request, pk):
instance = self.get_object()
instance.scheduled = utils.angular_datepicker(request.data['scheduled'])
instance.visit_type = request.data['visit_type']
instance.save()
instance_serialized = self.get_serializer(instance)
return Response(instance_serialized.data)
def destroy(self, request, pk):
instance = self.get_object()
instance.set_status('deleted')
instance_serialized = self.get_serializer(instance)
return Response(instance_serialized.data)
|
tperrier/mwachx
|
contacts/serializers/visits.py
|
Python
|
apache-2.0
| 4,316
|
[
"VisIt"
] |
21b3b11b2c81f8a0c6a26f9caea6fc853c78a8e2200fbf05b90c877c4dc7ce6d
|
""" SiteInspectorAgent
This agent inspect Sites, and evaluates policies that apply.
The following options can be set for the SiteInspectorAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN SiteInspectorAgent
:end-before: ##END
:dedent: 2
:caption: SiteInspectorAgent options
"""
__RCSID__ = '$Id$'
import math
import Queue
from DIRAC import S_OK
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.Core.Utilities.ThreadPool import ThreadPool
from DIRAC.Core.Utilities.ObjectLoader import ObjectLoader
from DIRAC.ResourceStatusSystem.PolicySystem.PEP import PEP
AGENT_NAME = 'ResourceStatus/SiteInspectorAgent'
class SiteInspectorAgent(AgentModule):
""" SiteInspectorAgent
The SiteInspectorAgent agent is an agent that is used to get the all the site names
and trigger PEP to evaluate their status.
"""
# Max number of worker threads by default
__maxNumberOfThreads = 15
# Inspection freqs, defaults, the lower, the higher priority to be checked.
# Error state usually means there is a glitch somewhere, so it has the highest
# priority.
__checkingFreqs = {'Active': 20,
'Degraded': 20,
'Probing': 20,
'Banned': 15,
'Unknown': 10,
'Error': 5}
def __init__(self, *args, **kwargs):
AgentModule.__init__(self, *args, **kwargs)
# ElementType, to be defined among Site, Resource or Node
self.sitesToBeChecked = None
self.threadPool = None
self.siteClient = None
self.clients = {}
def initialize(self):
""" Standard initialize.
"""
maxNumberOfThreads = self.am_getOption('maxNumberOfThreads', self.__maxNumberOfThreads)
self.threadPool = ThreadPool(maxNumberOfThreads, maxNumberOfThreads)
res = ObjectLoader().loadObject('DIRAC.ResourceStatusSystem.Client.SiteStatus',
'SiteStatus')
if not res['OK']:
self.log.error('Failed to load SiteStatus class: %s' % res['Message'])
return res
siteStatusClass = res['Value']
res = ObjectLoader().loadObject('DIRAC.ResourceStatusSystem.Client.ResourceManagementClient',
'ResourceManagementClient')
if not res['OK']:
self.log.error('Failed to load ResourceManagementClient class: %s' % res['Message'])
return res
rmClass = res['Value']
self.siteClient = siteStatusClass()
self.clients['SiteStatus'] = siteStatusClass()
self.clients['ResourceManagementClient'] = rmClass()
return S_OK()
def execute(self):
""" execute
This is the main method of the agent. It gets the sites from the Database, calculates how many threads should be
started and spawns them. Each thread will get a site from the queue until
it is empty. At the end, the method will join the queue such that the agent
will not terminate a cycle until all sites have been processed.
"""
# Gets sites to be checked ( returns a Queue )
sitesToBeChecked = self.getSitesToBeChecked()
if not sitesToBeChecked['OK']:
self.log.error(sitesToBeChecked['Message'])
return sitesToBeChecked
self.sitesToBeChecked = sitesToBeChecked['Value']
queueSize = self.sitesToBeChecked.qsize()
pollingTime = self.am_getPollingTime()
# Assigns number of threads on the fly such that we exhaust the PollingTime
# without having to spawn too many threads. We assume 10 seconds per element
# to be processed ( actually, it takes something like 1 sec per element ):
# numberOfThreads = elements * 10(s/element) / pollingTime
numberOfThreads = int(math.ceil(queueSize * 10. / pollingTime))
self.log.info('Needed %d threads to process %d elements' % (numberOfThreads, queueSize))
for _x in xrange(numberOfThreads):
jobUp = self.threadPool.generateJobAndQueueIt(self._execute)
if not jobUp['OK']:
self.log.error(jobUp['Message'])
self.log.info('blocking until all sites have been processed')
# block until all tasks are done
self.sitesToBeChecked.join()
self.log.info('done')
return S_OK()
def getSitesToBeChecked(self):
""" getElementsToBeChecked
This method gets all the site names from the SiteStatus table, after that it get the details of each
site (status, name, etc..) and adds them to a queue.
"""
toBeChecked = Queue.Queue()
res = self.siteClient.getSites('All')
if not res['OK']:
return res
# get the current status
res = self.siteClient.getSiteStatuses(res['Value'])
if not res['OK']:
return res
# filter elements
for site in res['Value']:
status = res['Value'].get(site, 'Unknown')
toBeChecked.put({'status': status,
'name': site,
'site': site,
'element': 'Site',
'statusType': 'all',
'elementType': 'Site'})
return S_OK(toBeChecked)
# Private methods ............................................................
def _execute(self):
"""
Method run by each of the thread that is in the ThreadPool.
It enters a loop until there are no sites on the queue.
On each iteration, it evaluates the policies for such site
and enforces the necessary actions. If there are no more sites in the
queue, the loop is finished.
"""
pep = PEP(clients=self.clients)
while True:
try:
site = self.sitesToBeChecked.get_nowait()
except Queue.Empty:
return S_OK()
resEnforce = pep.enforce(site)
if not resEnforce['OK']:
self.log.error('Failed policy enforcement', resEnforce['Message'])
self.sitesToBeChecked.task_done()
continue
# Used together with join !
self.sitesToBeChecked.task_done()
|
petricm/DIRAC
|
ResourceStatusSystem/Agent/SiteInspectorAgent.py
|
Python
|
gpl-3.0
| 5,884
|
[
"DIRAC"
] |
c4ae04d7bafe2e3a1d6fb29427c40b4564cc5333ea4b00ab809d64dd82147c17
|
#!/usr/bin/env python
"""
PyVTK provides tools for manipulating VTK files in Python.
VtkData - create VTK files from Python / read VTK files to Python
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revision: 1.11 $
$Date: 2003-04-07 14:56:08 $
Pearu Peterson
"""
__author__ = "Pearu Peterson <pearu@cens.ioc.ee>"
__license__ = "LGPL (see http://www.fsf.org)"
from .__version__ import __version__
__all__ = ['StructuredPoints','StructuredGrid','UnstructuredGrid',
'RectilinearGrid','PolyData',
'Scalars','ColorScalars','LookupTable','Vectors','Normals',
'TextureCoordinates','Tensors','Field',
'PointData','CellData',
'VtkData']
import types
import os
from . import common
from .StructuredPoints import StructuredPoints, structured_points_fromfile
from .StructuredGrid import StructuredGrid, structured_grid_fromfile
from .UnstructuredGrid import UnstructuredGrid, unstructured_grid_fromfile
from .RectilinearGrid import RectilinearGrid, rectilinear_grid_fromfile
from .PolyData import PolyData, polydata_fromfile
from .Scalars import Scalars,scalars_fromfile
from .ColorScalars import ColorScalars, color_scalars_fromfile
from .LookupTable import LookupTable, lookup_table_fromfile
from .Vectors import Vectors, vectors_fromfile
from .Normals import Normals, normals_fromfile
from .TextureCoordinates import TextureCoordinates, texture_coordinates_fromfile
from .Tensors import Tensors, tensors_fromfile
from .Field import Field, field_fromfile
from .Data import PointData,CellData
class VtkData(common.Common):
"""
VtkData
=======
Represents VTK file that has four relevant parts:
header - string up to length 255
format - string: ascii | binary
DataSet - StructuredPoints | StructuredGrid | UnstructuredGrid
| RectilinearGrid | PolyData
Data - PointData | CellData
Usage:
------
v = VtkData(<DataSet instance> [,<header string>,<Data instances>,..])
v = VtkData(<filename>, only_structure = 0) - read VTK data from file.
v.tofile(filename, format = 'ascii') - save VTK data to file.
Attributes:
header
structure
point_data
cell_data
Public methods:
to_string(format = 'ascii')
tofile(filename, format = 'ascii')
DataSet
=======
StructuredPoints(<3-sequence of dimensions>
[,<3-sequence of origin> [, <3-sequence of spacing>]])
StructuredGrid(<3-sequence of dimensions>,
<sequence of 3-sequences of points>)
UnstructuredGrid(<sequence of 3-sequences of points>
[,<cell> = <sequence of (sequences of) integers>])
cell - vertex | poly_vertex | line | poly_line | triangle
| triangle_strip | polygon | pixel | quad | tetra
| voxel | hexahedron | wedge | pyramid
RectilinearGrid([x = <sequence of x-coordinates>],
[y = <sequence of y-coordinates>],
[z = <sequence of z-coordinates>])
PolyData(<sequence of 3-sequences of points>,
[vertices = <sequence of (sequences of) integers>],
[lines = <sequence of (sequences of) integers>],
[polygons = <sequence of (sequences of) integers>],
[triangle_strips = <sequence of (sequences of) integers>])
Data
====
PointData | CellData ([<DataSetAttr instances>]) - construct Data instance
DataSetAttr
===========
DataSetAttr - Scalars | ColorScalars | LookupTable | Vectors
| Normals | TextureCoordinates | Tensors | Field
Scalars(<sequence of scalars> [,name[, lookup_table]])
ColorScalars(<sequence of scalar sequences> [,name])
LookupTable(<sequence of 4-sequences> [,name])
Vectors(<sequence of 3-sequences> [,name])
Normals(<sequence of 3-sequences> [,name])
TextureCoordinates(<sequence of (1,2, or 3)-sequences> [,name])
Tensors(<sequence of (3x3)-sequences> [,name])
Field([name,] [arrayname_1 = sequence of n_1-sequences, ...
arrayname_m = sequence of n_m-sequences,])
where len(array_1) == .. == len(array_m) must hold.
"""
header = None
point_data = None
cell_data = None
def __init__(self,*args,**kws):
assert args,'expected at least one argument'
if type(args[0]) is bytes:
if 'only_structure' in kws and kws['only_structure']:
self.fromfile(args[0],1)
else:
self.fromfile(args[0])
return
else:
structure = args[0]
args = list(args)[1:]
if not common.is_dataset(structure):
raise TypeError('argument structure must be StructuredPoints|StructuredGrid|UnstructuredGrid|RectilinearGrid|PolyData but got %s'%(type(structure)))
self.structure = structure
for a in args:
if common.is_string(a):
if len(a)>255:
self.skipping('striping header string to a length =255')
self.header = a[:255]
elif common.is_pointdata(a):
self.point_data = a
elif common.is_celldata(a):
self.cell_data = a
else:
self.skipping('unexpexted argument %s'%(type(a)))
if self.header is None:
self.header = 'Really cool data'
self.warning('Using header=%s'%(repr(self.header)))
if self.point_data is None and self.cell_data is None:
self.warning('No data defined')
if self.point_data is not None:
s = self.structure.get_size()
s1 = self.point_data.get_size()
if s1 != s:
raise ValueError('DataSet (size=%s) and PointData (size=%s) have different sizes'%(s,s1))
else:
self.point_data = PointData()
if self.cell_data is not None:
s = self.structure.get_cell_size()
s1 = self.cell_data.get_size()
if s1 != s:
raise ValueError('DataSet (cell_size=%s) and CellData (size=%s) have different sizes'%(s,s1))
else:
self.cell_data = CellData()
def to_string(self, format = 'ascii'):
ret = ['# vtk DataFile Version 2.0',
self.header,
format.upper(),
self.structure.to_string(format)
]
if self.cell_data.data:
ret.append(self.cell_data.to_string(format))
if self.point_data.data:
ret.append(self.point_data.to_string(format))
#print `ret`
return '\n'.join(ret)
def tofile(self, filename, format = 'ascii'):
"""Save VTK data to file.
"""
if not common.is_string(filename):
raise TypeError('argument filename must be string but got %s'%(type(filename)))
if format not in ['ascii','binary']:
raise TypeError('argument format must be ascii | binary')
filename = filename.strip()
if not filename:
raise ValueError('filename must be non-empty string')
if filename[-4:]!='.vtk':
filename += '.vtk'
#print 'Creating file',`filename`
f = open(filename,'wb')
f.write(self.to_string(format))
f.close()
def fromfile(self,filename, only_structure = 0):
filename = filename.strip()
if filename[-4:]!='.vtk':
filename += '.vtk'
#print 'Reading file',`filename`
f = open(filename,'rb')
l = f.readline()
if not l.strip().replace(' ','').lower() == '#vtkdatafileversion2.0':
raise TypeError('File '+repr(filename)+' is not VTK 2.0 format')
self.header = f.readline().rstrip()
format = f.readline().strip().lower()
if format not in ['ascii','binary']:
raise ValueError('Expected ascii|binary but got %s'%(repr(format)))
if format == 'binary':
raise NotImplementedError('reading vtk binary format')
l = common._getline(f).lower().split(' ')
if l[0].strip() != 'dataset':
raise ValueError('expected dataset but got %s'%(l[0]))
try:
ff = eval(l[1]+'_fromfile')
except NameError:
raise NotImplementedError('%s_fromfile'%(l[1]))
self.structure,l = ff(f,self)
for i in range(2):
if only_structure: break
if not l: break
l = [s.strip() for s in l.lower().split(' ')]
assert len(l)==2 and l[0] in ['cell_data','point_data'], l[0]
data = l[0]
n = eval(l[1])
lst = []
while 1:
l = common._getline(f)
if not l: break
sl = [s.strip() for s in l.split()]
k = sl[0].lower()
if k not in ['scalars','color_scalars','lookup_table','vectors',
'normals','texture_coordinates','tensors','field']:
break
try:
ff = eval(k+'_fromfile')
except NameError:
raise NotImplementedError('%s_fromfile'%(k))
lst.append(ff(f,n,sl[1:]))
if data == 'point_data':
self.point_data = PointData(*lst)
if data == 'cell_data':
self.cell_data = CellData(*lst)
if self.point_data is None:
self.point_data = PointData()
if self.cell_data is None:
self.cell_data = CellData()
f.close()
if __name__ == "__main__":
vtk = VtkData(StructuredPoints((3,1,1)),
'This is title',
PointData(Scalars([3,4,5]))
)
vtk.tofile('test')
|
ddempsey/PyFEHM
|
pyvtk/__init__.py
|
Python
|
lgpl-2.1
| 10,343
|
[
"VTK"
] |
150457fcad793f101fbbb3d32eb14ba44161b9bcc5d7eefc8d8d96b402a63a92
|
#!/usr/bin/env python3
import arbor
import argparse
import numpy as np
import pandas
import seaborn # You may have to pip install these.
class Cable(arbor.recipe):
def __init__(self, probes,
Vm, length, radius, cm, rL, g,
stimulus_start, stimulus_duration, stimulus_amplitude,
cv_policy_max_extent):
"""
probes -- list of probes
Vm -- membrane leak potential
length -- length of cable in μm
radius -- radius of cable in μm
cm -- membrane capacitance in F/m^2
rL -- axial resistivity in Ω·cm
g -- membrane conductivity in S/cm^2
stimulus_start -- start of stimulus in ms
stimulus_duration -- duration of stimulus in ms
stimulus_amplitude -- amplitude of stimulus in nA
cv_policy_max_extent -- maximum extent of control volume in μm
"""
# (4.1) The base C++ class constructor must be called first, to ensure that
# all memory in the C++ class is initialized correctly.
arbor.recipe.__init__(self)
self.the_probes = probes
self.Vm = Vm
self.length = length
self.radius = radius
self.cm = cm
self.rL = rL
self.g = g
self.stimulus_start = stimulus_start
self.stimulus_duration = stimulus_duration
self.stimulus_amplitude = stimulus_amplitude
self.cv_policy_max_extent = cv_policy_max_extent
self.the_props = arbor.neuron_cable_properties()
self.the_cat = arbor.default_catalogue()
self.the_props.register(self.the_cat)
def num_cells(self):
return 1
def num_sources(self, gid):
assert gid == 0
return 0
def cell_kind(self, gid):
assert gid == 0
return arbor.cell_kind.cable
def cell_description(self, gid):
"""A high level description of the cell with global identifier gid.
For example the morphology, synapses and ion channels required
to build a multi-compartment neuron.
"""
assert gid == 0
tree = arbor.segment_tree()
tree.append(arbor.mnpos,
arbor.mpoint(0, 0, 0, self.radius),
arbor.mpoint(self.length, 0, 0, self.radius),
tag=1)
labels = arbor.label_dict({'cable': '(tag 1)',
'start': '(location 0 0)'})
decor = arbor.decor()
decor.set_property(Vm=self.Vm)
decor.set_property(cm=self.cm)
decor.set_property(rL=self.rL)
decor.paint('"cable"',
arbor.density(f'pas/e={self.Vm}', {'g': self.g}))
decor.place('"start"', arbor.iclamp(self.stimulus_start, self.stimulus_duration, self.stimulus_amplitude), "iclamp")
policy = arbor.cv_policy_max_extent(self.cv_policy_max_extent)
decor.discretization(policy)
return arbor.cable_cell(tree, labels, decor)
def probes(self, gid):
assert gid == 0
return self.the_probes
def global_properties(self, kind):
return self.the_props
def get_rm(g):
"""Return membrane resistivity in Ohm*m^2
g -- membrane conductivity in S/m^2
"""
return 1/g
def get_taum(cm, rm):
"""Return membrane time constant in seconds
cm -- membrane capacitance in F/m^2
rm -- membrane resistivity in Ohm*m^2
"""
return cm*rm
def get_lambdam(a, rm, rL):
"""Return electronic length in m
a -- cable radius in m
rm -- membrane resistivity in Ohm*m^2
rL -- axial resistivity in Ohm*m
"""
return np.sqrt(a*rm/(2*rL))
def get_vcond(lambdam, taum):
"""Return conductance velocity in m/s
lambda -- electronic length in m
taum -- membrane time constant
"""
return 2*lambdam/taum
def get_tmax(data):
"""Return time of maximum of membrane voltage"""
return data[np.argmax(data[:, 1])][0]
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Cable')
parser.add_argument(
'--Vm', help="membrane leak potential in mV", type=float, default=-65)
parser.add_argument(
'--length', help="cable length in μm", type=float, default=1000)
parser.add_argument(
'--radius', help="cable radius in μm", type=float, default=1)
parser.add_argument(
'--cm', help="membrane capacitance in F/m^2", type=float, default=0.01)
parser.add_argument(
'--rL', help="axial resistivity in Ω·cm", type=float, default=90)
parser.add_argument(
'--g', help="membrane conductivity in S/cm^2", type=float, default=0.001)
parser.add_argument('--stimulus_start',
help="start of stimulus in ms", type=float, default=10)
parser.add_argument('--stimulus_duration',
help="duration of stimulus in ms", type=float, default=0.1)
parser.add_argument('--stimulus_amplitude',
help="amplitude of stimulus in nA", type=float, default=1)
parser.add_argument('--cv_policy_max_extent',
help="maximum extent of control volume in μm", type=float,
default=10)
# parse the command line arguments
args = parser.parse_args()
# set up membrane voltage probes equidistantly along the dendrites
probes = [arbor.cable_probe_membrane_voltage(
f'(location 0 {r})') for r in np.linspace(0, 1, 11)]
recipe = Cable(probes, **vars(args))
# create a default execution context and a default domain decomposition
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# configure the simulation and handles for the probes
sim = arbor.simulation(recipe, domains, context)
dt = 0.001
handles = [sim.sample((0, i), arbor.regular_schedule(dt))
for i in range(len(probes))]
# run the simulation for 30 ms
sim.run(tfinal=30, dt=dt)
# retrieve the sampled membrane voltages and convert to a pandas DataFrame
print("Plotting results ...")
df_list = []
for probe in range(len(handles)):
samples, meta = sim.samples(handles[probe])[0]
df_list.append(pandas.DataFrame({'t/ms': samples[:, 0], 'U/mV': samples[:, 1], 'Probe': f"{probe}"}))
df = pandas.concat(df_list,ignore_index=True)
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Probe",ci=None).set(xlim=(9,14)).savefig('single_cell_cable_result.svg')
# calculcate the idealized conduction velocity, cf. cable equation
data = [sim.samples(handle)[0][0] for handle in handles]
rm = get_rm(args.g*1/(0.01*0.01))
taum = get_taum(args.cm, rm)
lambdam = get_lambdam(args.radius*1e-6, rm, args.rL*0.01)
vcond_ideal = get_vcond(lambdam, taum)
# take the last and second probe
delta_t = (get_tmax(data[-1]) - get_tmax(data[1]))
# 90% because we took the second probe
delta_x = args.length*0.9
vcond = delta_x*1e-6/(delta_t*1e-3)
print(f"calculated conduction velocity: {vcond_ideal:.2f} m/s")
print(f"simulated conduction velocity: {vcond:.2f} m/s")
|
halfflat/nestmc-proto
|
python/example/single_cell_cable.py
|
Python
|
bsd-3-clause
| 7,141
|
[
"NEURON"
] |
ac45f37b64bacc78454aced5404677a428200c14e78dafbc384da85f427c0ccd
|
import numpy
from trefoil.analysis.summary import summarize_areas_by_category, calculate_weighted_statistics
from trefoil.utilities.window import Window
# Days per month from Tim, starting with January. Useful for weighting statistics when rolling months up to year.
# Assumes 365 day calendar with no leap years
DAYS_PER_MONTH = (31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31)
MONTH_LABELS = ('Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec')
def extract_categorical_timeseries_by_area(values, areas, timestep_indicies, window=None):
"""
Extract a timeseries array for each category found within the values of variable, using the areas occupied by
each category within each pixel.
:param values: the values for a given variable from the netcdf file. Must be organized on only 3 dimensions: time, row, col
:param areas: the areas of each pixel to count toward total area of given category in each timestep
:param timestep_indicies: the indices over which to extract the time series from the values of variable
#:param row_offset: the offset from the starting row coordinate of values to the starting row coordinate of areas
#:param col_offset: the offset from the starting column coordinate of values to the starting column coordinate of areas
:param window: the subdomain coordinates of areas within values. Must
:return: a dictionary of the categorical values found, each with a full timeseries
"""
assert len(values.shape) == 3
if window is not None:
assert isinstance(window, Window)
results = dict()
num_timesteps = len(timestep_indicies)
for index in timestep_indicies:
if window is not None:
data = window.clip(values, index).ravel()
else:
data = values[index].ravel()
data = numpy.ma.masked_array(data, mask=areas.mask)
category_summary = summarize_areas_by_category(data.astype("i"), areas)
for category in category_summary:
if not category in results:
results[category] = numpy.zeros(num_timesteps)
results[category][index] = category_summary[category]
return results
def extract_statistics_timeseries_by_weight(values, weights, statistics, window=None):
"""
Extract weighted time series statistics,
:param values: the values for a given variable from the netcdf file. Must be organized on only 3 dimensions: time, row, col
:param weights: the weight of each pixel for the statistic
:param statistics: a tuple indicating the statistics to be calculated, e.g., ("MEAN", "STD"). Note: statistics
do not account for different weights between time periods (e.g., months of different durations).
:param window: the subdomain coordinates of areas within values.
:return: a dictionary of statistic name to time series array
"""
assert len(values.shape) == 3
if window is not None:
assert isinstance(window, Window)
results = dict()
for statistic in statistics:
results[statistic] = numpy.zeros(values.shape[0])
for index in xrange(values.shape[0]):
if window is not None:
data = window.clip(values, index).ravel()
else:
data = values[index].ravel()
data = numpy.ma.masked_array(data, mask=weights.mask)
statistics_results = calculate_weighted_statistics(data, weights, statistics)
for stat_index, statistic in enumerate(statistics):
results[statistic][index] = statistics_results[stat_index]
return results
def linear_regression(timesteps, values, full=False):
"""Perform linear regression using linear algebra operators
Note: does not account for missing data within time series.
:param timesteps: 1D array of timesteps to use for x value of linear regression
:param values: 3D array of data to use for y value of linear regression, assumes timestep is first axis
:param full: return full statistics or just slopes & intercepts. Default is False. If True, requires scipy.
:returns: (slopes, intercepts) or (slopes, intercepts, r-squared, p-value) if full is True
"""
# ideas from:
# http://stackoverflow.com/questions/20343500/efficient-1d-linear-regression-for-each-element-of-3d-numpy-array
# http://stackoverflow.com/questions/3054191/converting-numpy-lstsq-residual-value-to-r2
# p-value calculation derived from scipy: https://github.com/scipy/scipy/blob/master/scipy/stats/stats.py
assert len(values.shape) == 3
assert values.shape[0] == timesteps.shape[0]
shape = values.shape
y = values.reshape((shape[0], shape[1] * shape[2]))
fit, residuals = numpy.linalg.lstsq(numpy.c_[timesteps, numpy.ones_like(timesteps)], y)[:2]
slopes = fit[0].reshape((shape[1], shape[2]))
intercepts = fit[1].reshape((shape[1], shape[2]))
mask = None
if hasattr(values, 'mask'):
mask = values.mask[0]
slopes = numpy.ma.masked_array(slopes, mask=mask)
intercepts = numpy.ma.masked_array(intercepts, mask=mask)
if not full:
return slopes, intercepts
# T-distribution used for p-value requires scipy
from scipy.stats.distributions import t as t_dist
# Calculate R2 value
r2 = (1 - residuals / (y.shape[0] * y.var(axis=0)))
r = numpy.sqrt(r2)
r2 = r2.reshape((shape[1], shape[2]))
# Calculate p-value
tiny = 1.0e-20
df = timesteps.shape[0] - 2
t = r * numpy.sqrt(df / ((1.0 - r + tiny)*(1.0 + r + tiny)))
p = (2 * t_dist.sf(numpy.abs(t), df)).reshape(shape[1], shape[2])
if mask is not None:
r2 = numpy.ma.masked_array(r2, mask=mask)
p = numpy.ma.masked_array(p, mask=mask)
return slopes, intercepts, r2, p
|
consbio/clover
|
trefoil/analysis/timeseries.py
|
Python
|
bsd-3-clause
| 5,913
|
[
"NetCDF"
] |
759b5a0bb2e9a69cbc1990d1879f2588e4c8fc584bf9ace383b435349dd54214
|
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
from sympy.core.relational import Relational
from sympy.core.sympify import sympify
from sympy.core.decorators import _sympifyit
from sympy.logic.boolalg import BooleanAtom
from sympy.polys.polyclasses import DMP
from sympy.polys.polyutils import (
basic_from_dict,
_sort_gens,
_unify_gens,
_dict_reorder,
_dict_from_expr,
_parallel_dict_from_expr,
)
from sympy.polys.rationaltools import together
from sympy.polys.rootisolation import dup_isolate_real_roots_list
from sympy.polys.groebnertools import groebner as _groebner
from sympy.polys.fglmtools import matrix_fglm
from sympy.polys.monomials import Monomial
from sympy.polys.orderings import monomial_key
from sympy.polys.polyerrors import (
OperationNotSupported, DomainError,
CoercionFailed, UnificationFailed,
GeneratorsNeeded, PolynomialError,
MultivariatePolynomialError,
ExactQuotientFailed,
PolificationFailed,
ComputationFailed,
GeneratorsError,
)
from sympy.utilities import group, sift, public
import sympy.polys
import mpmath
from mpmath.libmp.libhyper import NoConvergence
from sympy.polys.domains import FF, QQ, ZZ
from sympy.polys.constructor import construct_domain
from sympy.polys import polyoptions as options
from sympy.core.compatibility import iterable, range
@public
class Poly(Expr):
"""Generic class for representing polynomial expressions. """
__slots__ = ['rep', 'gens']
is_commutative = True
is_Poly = True
def __new__(cls, rep, *gens, **args):
"""Create a new polynomial instance out of something useful. """
opt = options.build_options(gens, args)
if 'order' in opt:
raise NotImplementedError("'order' keyword is not implemented yet")
if iterable(rep, exclude=str):
if isinstance(rep, dict):
return cls._from_dict(rep, opt)
else:
return cls._from_list(list(rep), opt)
else:
rep = sympify(rep)
if rep.is_Poly:
return cls._from_poly(rep, opt)
else:
return cls._from_expr(rep, opt)
@classmethod
def new(cls, rep, *gens):
"""Construct :class:`Poly` instance from raw representation. """
if not isinstance(rep, DMP):
raise PolynomialError(
"invalid polynomial representation: %s" % rep)
elif rep.lev != len(gens) - 1:
raise PolynomialError("invalid arguments: %s, %s" % (rep, gens))
obj = Basic.__new__(cls)
obj.rep = rep
obj.gens = gens
return obj
@classmethod
def from_dict(cls, rep, *gens, **args):
"""Construct a polynomial from a ``dict``. """
opt = options.build_options(gens, args)
return cls._from_dict(rep, opt)
@classmethod
def from_list(cls, rep, *gens, **args):
"""Construct a polynomial from a ``list``. """
opt = options.build_options(gens, args)
return cls._from_list(rep, opt)
@classmethod
def from_poly(cls, rep, *gens, **args):
"""Construct a polynomial from a polynomial. """
opt = options.build_options(gens, args)
return cls._from_poly(rep, opt)
@classmethod
def from_expr(cls, rep, *gens, **args):
"""Construct a polynomial from an expression. """
opt = options.build_options(gens, args)
return cls._from_expr(rep, opt)
@classmethod
def _from_dict(cls, rep, opt):
"""Construct a polynomial from a ``dict``. """
gens = opt.gens
if not gens:
raise GeneratorsNeeded(
"can't initialize from 'dict' without generators")
level = len(gens) - 1
domain = opt.domain
if domain is None:
domain, rep = construct_domain(rep, opt=opt)
else:
for monom, coeff in rep.items():
rep[monom] = domain.convert(coeff)
return cls.new(DMP.from_dict(rep, level, domain), *gens)
@classmethod
def _from_list(cls, rep, opt):
"""Construct a polynomial from a ``list``. """
gens = opt.gens
if not gens:
raise GeneratorsNeeded(
"can't initialize from 'list' without generators")
elif len(gens) != 1:
raise MultivariatePolynomialError(
"'list' representation not supported")
level = len(gens) - 1
domain = opt.domain
if domain is None:
domain, rep = construct_domain(rep, opt=opt)
else:
rep = list(map(domain.convert, rep))
return cls.new(DMP.from_list(rep, level, domain), *gens)
@classmethod
def _from_poly(cls, rep, opt):
"""Construct a polynomial from a polynomial. """
if cls != rep.__class__:
rep = cls.new(rep.rep, *rep.gens)
gens = opt.gens
field = opt.field
domain = opt.domain
if gens and rep.gens != gens:
if set(rep.gens) != set(gens):
return cls._from_expr(rep.as_expr(), opt)
else:
rep = rep.reorder(*gens)
if 'domain' in opt and domain:
rep = rep.set_domain(domain)
elif field is True:
rep = rep.to_field()
return rep
@classmethod
def _from_expr(cls, rep, opt):
"""Construct a polynomial from an expression. """
rep, opt = _dict_from_expr(rep, opt)
return cls._from_dict(rep, opt)
def _hashable_content(self):
"""Allow SymPy to hash Poly instances. """
return (self.rep, self.gens)
def __hash__(self):
return super(Poly, self).__hash__()
@property
def free_symbols(self):
"""
Free symbols of a polynomial expression.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 1).free_symbols
set([x])
>>> Poly(x**2 + y).free_symbols
set([x, y])
>>> Poly(x**2 + y, x).free_symbols
set([x, y])
"""
symbols = set([])
for gen in self.gens:
symbols |= gen.free_symbols
return symbols | self.free_symbols_in_domain
@property
def free_symbols_in_domain(self):
"""
Free symbols of the domain of ``self``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 1).free_symbols_in_domain
set()
>>> Poly(x**2 + y).free_symbols_in_domain
set()
>>> Poly(x**2 + y, x).free_symbols_in_domain
set([y])
"""
domain, symbols = self.rep.dom, set()
if domain.is_Composite:
for gen in domain.symbols:
symbols |= gen.free_symbols
elif domain.is_EX:
for coeff in self.coeffs():
symbols |= coeff.free_symbols
return symbols
@property
def args(self):
"""
Don't mess up with the core.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).args
(x**2 + 1,)
"""
return (self.as_expr(),)
@property
def gen(self):
"""
Return the principal generator.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).gen
x
"""
return self.gens[0]
@property
def domain(self):
"""Get the ground domain of ``self``. """
return self.get_domain()
@property
def zero(self):
"""Return zero polynomial with ``self``'s properties. """
return self.new(self.rep.zero(self.rep.lev, self.rep.dom), *self.gens)
@property
def one(self):
"""Return one polynomial with ``self``'s properties. """
return self.new(self.rep.one(self.rep.lev, self.rep.dom), *self.gens)
@property
def unit(self):
"""Return unit polynomial with ``self``'s properties. """
return self.new(self.rep.unit(self.rep.lev, self.rep.dom), *self.gens)
def unify(f, g):
"""
Make ``f`` and ``g`` belong to the same domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f, g = Poly(x/2 + 1), Poly(2*x + 1)
>>> f
Poly(1/2*x + 1, x, domain='QQ')
>>> g
Poly(2*x + 1, x, domain='ZZ')
>>> F, G = f.unify(g)
>>> F
Poly(1/2*x + 1, x, domain='QQ')
>>> G
Poly(2*x + 1, x, domain='QQ')
"""
_, per, F, G = f._unify(g)
return per(F), per(G)
def _unify(f, g):
g = sympify(g)
if not g.is_Poly:
try:
return f.rep.dom, f.per, f.rep, f.rep.per(f.rep.dom.from_sympy(g))
except CoercionFailed:
raise UnificationFailed("can't unify %s with %s" % (f, g))
if isinstance(f.rep, DMP) and isinstance(g.rep, DMP):
gens = _unify_gens(f.gens, g.gens)
dom, lev = f.rep.dom.unify(g.rep.dom, gens), len(gens) - 1
if f.gens != gens:
f_monoms, f_coeffs = _dict_reorder(
f.rep.to_dict(), f.gens, gens)
if f.rep.dom != dom:
f_coeffs = [dom.convert(c, f.rep.dom) for c in f_coeffs]
F = DMP(dict(list(zip(f_monoms, f_coeffs))), dom, lev)
else:
F = f.rep.convert(dom)
if g.gens != gens:
g_monoms, g_coeffs = _dict_reorder(
g.rep.to_dict(), g.gens, gens)
if g.rep.dom != dom:
g_coeffs = [dom.convert(c, g.rep.dom) for c in g_coeffs]
G = DMP(dict(list(zip(g_monoms, g_coeffs))), dom, lev)
else:
G = g.rep.convert(dom)
else:
raise UnificationFailed("can't unify %s with %s" % (f, g))
cls = f.__class__
def per(rep, dom=dom, gens=gens, remove=None):
if remove is not None:
gens = gens[:remove] + gens[remove + 1:]
if not gens:
return dom.to_sympy(rep)
return cls.new(rep, *gens)
return dom, per, F, G
def per(f, rep, gens=None, remove=None):
"""
Create a Poly out of the given representation.
Examples
========
>>> from sympy import Poly, ZZ
>>> from sympy.abc import x, y
>>> from sympy.polys.polyclasses import DMP
>>> a = Poly(x**2 + 1)
>>> a.per(DMP([ZZ(1), ZZ(1)], ZZ), gens=[y])
Poly(y + 1, y, domain='ZZ')
"""
if gens is None:
gens = f.gens
if remove is not None:
gens = gens[:remove] + gens[remove + 1:]
if not gens:
return f.rep.dom.to_sympy(rep)
return f.__class__.new(rep, *gens)
def set_domain(f, domain):
"""Set the ground domain of ``f``. """
opt = options.build_options(f.gens, {'domain': domain})
return f.per(f.rep.convert(opt.domain))
def get_domain(f):
"""Get the ground domain of ``f``. """
return f.rep.dom
def set_modulus(f, modulus):
"""
Set the modulus of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(5*x**2 + 2*x - 1, x).set_modulus(2)
Poly(x**2 + 1, x, modulus=2)
"""
modulus = options.Modulus.preprocess(modulus)
return f.set_domain(FF(modulus))
def get_modulus(f):
"""
Get the modulus of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, modulus=2).get_modulus()
2
"""
domain = f.get_domain()
if domain.is_FiniteField:
return Integer(domain.characteristic())
else:
raise PolynomialError("not a polynomial over a Galois field")
def _eval_subs(f, old, new):
"""Internal implementation of :func:`subs`. """
if old in f.gens:
if new.is_number:
return f.eval(old, new)
else:
try:
return f.replace(old, new)
except PolynomialError:
pass
return f.as_expr().subs(old, new)
def exclude(f):
"""
Remove unnecessary generators from ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import a, b, c, d, x
>>> Poly(a + x, a, b, c, d, x).exclude()
Poly(a + x, a, x, domain='ZZ')
"""
J, new = f.rep.exclude()
gens = []
for j in range(len(f.gens)):
if j not in J:
gens.append(f.gens[j])
return f.per(new, gens=gens)
def replace(f, x, y=None):
"""
Replace ``x`` with ``y`` in generators list.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 1, x).replace(x, y)
Poly(y**2 + 1, y, domain='ZZ')
"""
if y is None:
if f.is_univariate:
x, y = f.gen, x
else:
raise PolynomialError(
"syntax supported only in univariate case")
if x == y:
return f
if x in f.gens and y not in f.gens:
dom = f.get_domain()
if not dom.is_Composite or y not in dom.symbols:
gens = list(f.gens)
gens[gens.index(x)] = y
return f.per(f.rep, gens=gens)
raise PolynomialError("can't replace %s with %s in %s" % (x, y, f))
def reorder(f, *gens, **args):
"""
Efficiently apply new order of generators.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + x*y**2, x, y).reorder(y, x)
Poly(y**2*x + x**2, y, x, domain='ZZ')
"""
opt = options.Options((), args)
if not gens:
gens = _sort_gens(f.gens, opt=opt)
elif set(f.gens) != set(gens):
raise PolynomialError(
"generators list can differ only up to order of elements")
rep = dict(list(zip(*_dict_reorder(f.rep.to_dict(), f.gens, gens))))
return f.per(DMP(rep, f.rep.dom, len(gens) - 1), gens=gens)
def ltrim(f, gen):
"""
Remove dummy generators from the "left" of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y, z
>>> Poly(y**2 + y*z**2, x, y, z).ltrim(y)
Poly(y**2 + y*z**2, y, z, domain='ZZ')
"""
rep = f.as_dict(native=True)
j = f._gen_to_level(gen)
terms = {}
for monom, coeff in rep.items():
monom = monom[j:]
if monom not in terms:
terms[monom] = coeff
else:
raise PolynomialError("can't left trim %s" % f)
gens = f.gens[j:]
return f.new(DMP.from_dict(terms, len(gens) - 1, f.rep.dom), *gens)
def has_only_gens(f, *gens):
"""
Return ``True`` if ``Poly(f, *gens)`` retains ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y, z
>>> Poly(x*y + 1, x, y, z).has_only_gens(x, y)
True
>>> Poly(x*y + z, x, y, z).has_only_gens(x, y)
False
"""
indices = set([])
for gen in gens:
try:
index = f.gens.index(gen)
except ValueError:
raise GeneratorsError(
"%s doesn't have %s as generator" % (f, gen))
else:
indices.add(index)
for monom in f.monoms():
for i, elt in enumerate(monom):
if i not in indices and elt:
return False
return True
def to_ring(f):
"""
Make the ground domain a ring.
Examples
========
>>> from sympy import Poly, QQ
>>> from sympy.abc import x
>>> Poly(x**2 + 1, domain=QQ).to_ring()
Poly(x**2 + 1, x, domain='ZZ')
"""
if hasattr(f.rep, 'to_ring'):
result = f.rep.to_ring()
else: # pragma: no cover
raise OperationNotSupported(f, 'to_ring')
return f.per(result)
def to_field(f):
"""
Make the ground domain a field.
Examples
========
>>> from sympy import Poly, ZZ
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x, domain=ZZ).to_field()
Poly(x**2 + 1, x, domain='QQ')
"""
if hasattr(f.rep, 'to_field'):
result = f.rep.to_field()
else: # pragma: no cover
raise OperationNotSupported(f, 'to_field')
return f.per(result)
def to_exact(f):
"""
Make the ground domain exact.
Examples
========
>>> from sympy import Poly, RR
>>> from sympy.abc import x
>>> Poly(x**2 + 1.0, x, domain=RR).to_exact()
Poly(x**2 + 1, x, domain='QQ')
"""
if hasattr(f.rep, 'to_exact'):
result = f.rep.to_exact()
else: # pragma: no cover
raise OperationNotSupported(f, 'to_exact')
return f.per(result)
def retract(f, field=None):
"""
Recalculate the ground domain of a polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = Poly(x**2 + 1, x, domain='QQ[y]')
>>> f
Poly(x**2 + 1, x, domain='QQ[y]')
>>> f.retract()
Poly(x**2 + 1, x, domain='ZZ')
>>> f.retract(field=True)
Poly(x**2 + 1, x, domain='QQ')
"""
dom, rep = construct_domain(f.as_dict(zero=True),
field=field, composite=f.domain.is_Composite or None)
return f.from_dict(rep, f.gens, domain=dom)
def slice(f, x, m, n=None):
"""Take a continuous subsequence of terms of ``f``. """
if n is None:
j, m, n = 0, x, m
else:
j = f._gen_to_level(x)
m, n = int(m), int(n)
if hasattr(f.rep, 'slice'):
result = f.rep.slice(m, n, j)
else: # pragma: no cover
raise OperationNotSupported(f, 'slice')
return f.per(result)
def coeffs(f, order=None):
"""
Returns all non-zero coefficients from ``f`` in lex order.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 + 2*x + 3, x).coeffs()
[1, 2, 3]
See Also
========
all_coeffs
coeff_monomial
nth
"""
return [f.rep.dom.to_sympy(c) for c in f.rep.coeffs(order=order)]
def monoms(f, order=None):
"""
Returns all non-zero monomials from ``f`` in lex order.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 2*x*y**2 + x*y + 3*y, x, y).monoms()
[(2, 0), (1, 2), (1, 1), (0, 1)]
See Also
========
all_monoms
"""
return f.rep.monoms(order=order)
def terms(f, order=None):
"""
Returns all non-zero terms from ``f`` in lex order.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 2*x*y**2 + x*y + 3*y, x, y).terms()
[((2, 0), 1), ((1, 2), 2), ((1, 1), 1), ((0, 1), 3)]
See Also
========
all_terms
"""
return [(m, f.rep.dom.to_sympy(c)) for m, c in f.rep.terms(order=order)]
def all_coeffs(f):
"""
Returns all coefficients from a univariate polynomial ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 + 2*x - 1, x).all_coeffs()
[1, 0, 2, -1]
"""
return [f.rep.dom.to_sympy(c) for c in f.rep.all_coeffs()]
def all_monoms(f):
"""
Returns all monomials from a univariate polynomial ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 + 2*x - 1, x).all_monoms()
[(3,), (2,), (1,), (0,)]
See Also
========
all_terms
"""
return f.rep.all_monoms()
def all_terms(f):
"""
Returns all terms from a univariate polynomial ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 + 2*x - 1, x).all_terms()
[((3,), 1), ((2,), 0), ((1,), 2), ((0,), -1)]
"""
return [(m, f.rep.dom.to_sympy(c)) for m, c in f.rep.all_terms()]
def termwise(f, func, *gens, **args):
"""
Apply a function to all terms of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> def func(k, coeff):
... k = k[0]
... return coeff//10**(2-k)
>>> Poly(x**2 + 20*x + 400).termwise(func)
Poly(x**2 + 2*x + 4, x, domain='ZZ')
"""
terms = {}
for monom, coeff in f.terms():
result = func(monom, coeff)
if isinstance(result, tuple):
monom, coeff = result
else:
coeff = result
if coeff:
if monom not in terms:
terms[monom] = coeff
else:
raise PolynomialError(
"%s monomial was generated twice" % monom)
return f.from_dict(terms, *(gens or f.gens), **args)
def length(f):
"""
Returns the number of non-zero terms in ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 2*x - 1).length()
3
"""
return len(f.as_dict())
def as_dict(f, native=False, zero=False):
"""
Switch to a ``dict`` representation.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 2*x*y**2 - y, x, y).as_dict()
{(0, 1): -1, (1, 2): 2, (2, 0): 1}
"""
if native:
return f.rep.to_dict(zero=zero)
else:
return f.rep.to_sympy_dict(zero=zero)
def as_list(f, native=False):
"""Switch to a ``list`` representation. """
if native:
return f.rep.to_list()
else:
return f.rep.to_sympy_list()
def as_expr(f, *gens):
"""
Convert a Poly instance to an Expr instance.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = Poly(x**2 + 2*x*y**2 - y, x, y)
>>> f.as_expr()
x**2 + 2*x*y**2 - y
>>> f.as_expr({x: 5})
10*y**2 - y + 25
>>> f.as_expr(5, 6)
379
"""
if not gens:
gens = f.gens
elif len(gens) == 1 and isinstance(gens[0], dict):
mapping = gens[0]
gens = list(f.gens)
for gen, value in mapping.items():
try:
index = gens.index(gen)
except ValueError:
raise GeneratorsError(
"%s doesn't have %s as generator" % (f, gen))
else:
gens[index] = value
return basic_from_dict(f.rep.to_sympy_dict(), *gens)
def lift(f):
"""
Convert algebraic coefficients to rationals.
Examples
========
>>> from sympy import Poly, I
>>> from sympy.abc import x
>>> Poly(x**2 + I*x + 1, x, extension=I).lift()
Poly(x**4 + 3*x**2 + 1, x, domain='QQ')
"""
if hasattr(f.rep, 'lift'):
result = f.rep.lift()
else: # pragma: no cover
raise OperationNotSupported(f, 'lift')
return f.per(result)
def deflate(f):
"""
Reduce degree of ``f`` by mapping ``x_i**m`` to ``y_i``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**6*y**2 + x**3 + 1, x, y).deflate()
((3, 2), Poly(x**2*y + x + 1, x, y, domain='ZZ'))
"""
if hasattr(f.rep, 'deflate'):
J, result = f.rep.deflate()
else: # pragma: no cover
raise OperationNotSupported(f, 'deflate')
return J, f.per(result)
def inject(f, front=False):
"""
Inject ground domain generators into ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = Poly(x**2*y + x*y**3 + x*y + 1, x)
>>> f.inject()
Poly(x**2*y + x*y**3 + x*y + 1, x, y, domain='ZZ')
>>> f.inject(front=True)
Poly(y**3*x + y*x**2 + y*x + 1, y, x, domain='ZZ')
"""
dom = f.rep.dom
if dom.is_Numerical:
return f
elif not dom.is_Poly:
raise DomainError("can't inject generators over %s" % dom)
if hasattr(f.rep, 'inject'):
result = f.rep.inject(front=front)
else: # pragma: no cover
raise OperationNotSupported(f, 'inject')
if front:
gens = dom.symbols + f.gens
else:
gens = f.gens + dom.symbols
return f.new(result, *gens)
def eject(f, *gens):
"""
Eject selected generators into the ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = Poly(x**2*y + x*y**3 + x*y + 1, x, y)
>>> f.eject(x)
Poly(x*y**3 + (x**2 + x)*y + 1, y, domain='ZZ[x]')
>>> f.eject(y)
Poly(y*x**2 + (y**3 + y)*x + 1, x, domain='ZZ[y]')
"""
dom = f.rep.dom
if not dom.is_Numerical:
raise DomainError("can't eject generators over %s" % dom)
n, k = len(f.gens), len(gens)
if f.gens[:k] == gens:
_gens, front = f.gens[k:], True
elif f.gens[-k:] == gens:
_gens, front = f.gens[:-k], False
else:
raise NotImplementedError(
"can only eject front or back generators")
dom = dom.inject(*gens)
if hasattr(f.rep, 'eject'):
result = f.rep.eject(dom, front=front)
else: # pragma: no cover
raise OperationNotSupported(f, 'eject')
return f.new(result, *_gens)
def terms_gcd(f):
"""
Remove GCD of terms from the polynomial ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**6*y**2 + x**3*y, x, y).terms_gcd()
((3, 1), Poly(x**3*y + 1, x, y, domain='ZZ'))
"""
if hasattr(f.rep, 'terms_gcd'):
J, result = f.rep.terms_gcd()
else: # pragma: no cover
raise OperationNotSupported(f, 'terms_gcd')
return J, f.per(result)
def add_ground(f, coeff):
"""
Add an element of the ground domain to ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x + 1).add_ground(2)
Poly(x + 3, x, domain='ZZ')
"""
if hasattr(f.rep, 'add_ground'):
result = f.rep.add_ground(coeff)
else: # pragma: no cover
raise OperationNotSupported(f, 'add_ground')
return f.per(result)
def sub_ground(f, coeff):
"""
Subtract an element of the ground domain from ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x + 1).sub_ground(2)
Poly(x - 1, x, domain='ZZ')
"""
if hasattr(f.rep, 'sub_ground'):
result = f.rep.sub_ground(coeff)
else: # pragma: no cover
raise OperationNotSupported(f, 'sub_ground')
return f.per(result)
def mul_ground(f, coeff):
"""
Multiply ``f`` by a an element of the ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x + 1).mul_ground(2)
Poly(2*x + 2, x, domain='ZZ')
"""
if hasattr(f.rep, 'mul_ground'):
result = f.rep.mul_ground(coeff)
else: # pragma: no cover
raise OperationNotSupported(f, 'mul_ground')
return f.per(result)
def quo_ground(f, coeff):
"""
Quotient of ``f`` by a an element of the ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x + 4).quo_ground(2)
Poly(x + 2, x, domain='ZZ')
>>> Poly(2*x + 3).quo_ground(2)
Poly(x + 1, x, domain='ZZ')
"""
if hasattr(f.rep, 'quo_ground'):
result = f.rep.quo_ground(coeff)
else: # pragma: no cover
raise OperationNotSupported(f, 'quo_ground')
return f.per(result)
def exquo_ground(f, coeff):
"""
Exact quotient of ``f`` by a an element of the ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x + 4).exquo_ground(2)
Poly(x + 2, x, domain='ZZ')
>>> Poly(2*x + 3).exquo_ground(2)
Traceback (most recent call last):
...
ExactQuotientFailed: 2 does not divide 3 in ZZ
"""
if hasattr(f.rep, 'exquo_ground'):
result = f.rep.exquo_ground(coeff)
else: # pragma: no cover
raise OperationNotSupported(f, 'exquo_ground')
return f.per(result)
def abs(f):
"""
Make all coefficients in ``f`` positive.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).abs()
Poly(x**2 + 1, x, domain='ZZ')
"""
if hasattr(f.rep, 'abs'):
result = f.rep.abs()
else: # pragma: no cover
raise OperationNotSupported(f, 'abs')
return f.per(result)
def neg(f):
"""
Negate all coefficients in ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).neg()
Poly(-x**2 + 1, x, domain='ZZ')
>>> -Poly(x**2 - 1, x)
Poly(-x**2 + 1, x, domain='ZZ')
"""
if hasattr(f.rep, 'neg'):
result = f.rep.neg()
else: # pragma: no cover
raise OperationNotSupported(f, 'neg')
return f.per(result)
def add(f, g):
"""
Add two polynomials ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).add(Poly(x - 2, x))
Poly(x**2 + x - 1, x, domain='ZZ')
>>> Poly(x**2 + 1, x) + Poly(x - 2, x)
Poly(x**2 + x - 1, x, domain='ZZ')
"""
g = sympify(g)
if not g.is_Poly:
return f.add_ground(g)
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'add'):
result = F.add(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'add')
return per(result)
def sub(f, g):
"""
Subtract two polynomials ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).sub(Poly(x - 2, x))
Poly(x**2 - x + 3, x, domain='ZZ')
>>> Poly(x**2 + 1, x) - Poly(x - 2, x)
Poly(x**2 - x + 3, x, domain='ZZ')
"""
g = sympify(g)
if not g.is_Poly:
return f.sub_ground(g)
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'sub'):
result = F.sub(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'sub')
return per(result)
def mul(f, g):
"""
Multiply two polynomials ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).mul(Poly(x - 2, x))
Poly(x**3 - 2*x**2 + x - 2, x, domain='ZZ')
>>> Poly(x**2 + 1, x)*Poly(x - 2, x)
Poly(x**3 - 2*x**2 + x - 2, x, domain='ZZ')
"""
g = sympify(g)
if not g.is_Poly:
return f.mul_ground(g)
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'mul'):
result = F.mul(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'mul')
return per(result)
def sqr(f):
"""
Square a polynomial ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x - 2, x).sqr()
Poly(x**2 - 4*x + 4, x, domain='ZZ')
>>> Poly(x - 2, x)**2
Poly(x**2 - 4*x + 4, x, domain='ZZ')
"""
if hasattr(f.rep, 'sqr'):
result = f.rep.sqr()
else: # pragma: no cover
raise OperationNotSupported(f, 'sqr')
return f.per(result)
def pow(f, n):
"""
Raise ``f`` to a non-negative power ``n``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x - 2, x).pow(3)
Poly(x**3 - 6*x**2 + 12*x - 8, x, domain='ZZ')
>>> Poly(x - 2, x)**3
Poly(x**3 - 6*x**2 + 12*x - 8, x, domain='ZZ')
"""
n = int(n)
if hasattr(f.rep, 'pow'):
result = f.rep.pow(n)
else: # pragma: no cover
raise OperationNotSupported(f, 'pow')
return f.per(result)
def pdiv(f, g):
"""
Polynomial pseudo-division of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).pdiv(Poly(2*x - 4, x))
(Poly(2*x + 4, x, domain='ZZ'), Poly(20, x, domain='ZZ'))
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'pdiv'):
q, r = F.pdiv(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'pdiv')
return per(q), per(r)
def prem(f, g):
"""
Polynomial pseudo-remainder of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).prem(Poly(2*x - 4, x))
Poly(20, x, domain='ZZ')
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'prem'):
result = F.prem(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'prem')
return per(result)
def pquo(f, g):
"""
Polynomial pseudo-quotient of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).pquo(Poly(2*x - 4, x))
Poly(2*x + 4, x, domain='ZZ')
>>> Poly(x**2 - 1, x).pquo(Poly(2*x - 2, x))
Poly(2*x + 2, x, domain='ZZ')
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'pquo'):
result = F.pquo(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'pquo')
return per(result)
def pexquo(f, g):
"""
Polynomial exact pseudo-quotient of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).pexquo(Poly(2*x - 2, x))
Poly(2*x + 2, x, domain='ZZ')
>>> Poly(x**2 + 1, x).pexquo(Poly(2*x - 4, x))
Traceback (most recent call last):
...
ExactQuotientFailed: 2*x - 4 does not divide x**2 + 1
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'pexquo'):
try:
result = F.pexquo(G)
except ExactQuotientFailed as exc:
raise exc.new(f.as_expr(), g.as_expr())
else: # pragma: no cover
raise OperationNotSupported(f, 'pexquo')
return per(result)
def div(f, g, auto=True):
"""
Polynomial division with remainder of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).div(Poly(2*x - 4, x))
(Poly(1/2*x + 1, x, domain='QQ'), Poly(5, x, domain='QQ'))
>>> Poly(x**2 + 1, x).div(Poly(2*x - 4, x), auto=False)
(Poly(0, x, domain='ZZ'), Poly(x**2 + 1, x, domain='ZZ'))
"""
dom, per, F, G = f._unify(g)
retract = False
if auto and dom.has_Ring and not dom.has_Field:
F, G = F.to_field(), G.to_field()
retract = True
if hasattr(f.rep, 'div'):
q, r = F.div(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'div')
if retract:
try:
Q, R = q.to_ring(), r.to_ring()
except CoercionFailed:
pass
else:
q, r = Q, R
return per(q), per(r)
def rem(f, g, auto=True):
"""
Computes the polynomial remainder of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).rem(Poly(2*x - 4, x))
Poly(5, x, domain='ZZ')
>>> Poly(x**2 + 1, x).rem(Poly(2*x - 4, x), auto=False)
Poly(x**2 + 1, x, domain='ZZ')
"""
dom, per, F, G = f._unify(g)
retract = False
if auto and dom.has_Ring and not dom.has_Field:
F, G = F.to_field(), G.to_field()
retract = True
if hasattr(f.rep, 'rem'):
r = F.rem(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'rem')
if retract:
try:
r = r.to_ring()
except CoercionFailed:
pass
return per(r)
def quo(f, g, auto=True):
"""
Computes polynomial quotient of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).quo(Poly(2*x - 4, x))
Poly(1/2*x + 1, x, domain='QQ')
>>> Poly(x**2 - 1, x).quo(Poly(x - 1, x))
Poly(x + 1, x, domain='ZZ')
"""
dom, per, F, G = f._unify(g)
retract = False
if auto and dom.has_Ring and not dom.has_Field:
F, G = F.to_field(), G.to_field()
retract = True
if hasattr(f.rep, 'quo'):
q = F.quo(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'quo')
if retract:
try:
q = q.to_ring()
except CoercionFailed:
pass
return per(q)
def exquo(f, g, auto=True):
"""
Computes polynomial exact quotient of ``f`` by ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).exquo(Poly(x - 1, x))
Poly(x + 1, x, domain='ZZ')
>>> Poly(x**2 + 1, x).exquo(Poly(2*x - 4, x))
Traceback (most recent call last):
...
ExactQuotientFailed: 2*x - 4 does not divide x**2 + 1
"""
dom, per, F, G = f._unify(g)
retract = False
if auto and dom.has_Ring and not dom.has_Field:
F, G = F.to_field(), G.to_field()
retract = True
if hasattr(f.rep, 'exquo'):
try:
q = F.exquo(G)
except ExactQuotientFailed as exc:
raise exc.new(f.as_expr(), g.as_expr())
else: # pragma: no cover
raise OperationNotSupported(f, 'exquo')
if retract:
try:
q = q.to_ring()
except CoercionFailed:
pass
return per(q)
def _gen_to_level(f, gen):
"""Returns level associated with the given generator. """
if isinstance(gen, int):
length = len(f.gens)
if -length <= gen < length:
if gen < 0:
return length + gen
else:
return gen
else:
raise PolynomialError("-%s <= gen < %s expected, got %s" %
(length, length, gen))
else:
try:
return f.gens.index(sympify(gen))
except ValueError:
raise PolynomialError(
"a valid generator expected, got %s" % gen)
def degree(f, gen=0):
"""
Returns degree of ``f`` in ``x_j``.
The degree of 0 is negative infinity.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + y*x + 1, x, y).degree()
2
>>> Poly(x**2 + y*x + y, x, y).degree(y)
1
>>> Poly(0, x).degree()
-oo
"""
j = f._gen_to_level(gen)
if hasattr(f.rep, 'degree'):
return f.rep.degree(j)
else: # pragma: no cover
raise OperationNotSupported(f, 'degree')
def degree_list(f):
"""
Returns a list of degrees of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + y*x + 1, x, y).degree_list()
(2, 1)
"""
if hasattr(f.rep, 'degree_list'):
return f.rep.degree_list()
else: # pragma: no cover
raise OperationNotSupported(f, 'degree_list')
def total_degree(f):
"""
Returns the total degree of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + y*x + 1, x, y).total_degree()
2
>>> Poly(x + y**5, x, y).total_degree()
5
"""
if hasattr(f.rep, 'total_degree'):
return f.rep.total_degree()
else: # pragma: no cover
raise OperationNotSupported(f, 'total_degree')
def homogenize(f, s):
"""
Returns the homogeneous polynomial of ``f``.
A homogeneous polynomial is a polynomial whose all monomials with
non-zero coefficients have the same total degree. If you only
want to check if a polynomial is homogeneous, then use
:func:`Poly.is_homogeneous`. If you want not only to check if a
polynomial is homogeneous but also compute its homogeneous order,
then use :func:`Poly.homogeneous_order`.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y, z
>>> f = Poly(x**5 + 2*x**2*y**2 + 9*x*y**3)
>>> f.homogenize(z)
Poly(x**5 + 2*x**2*y**2*z + 9*x*y**3*z, x, y, z, domain='ZZ')
"""
if not isinstance(s, Symbol):
raise TypeError("``Symbol`` expected, got %s" % type(s))
if s in f.gens:
i = f.gens.index(s)
gens = f.gens
else:
i = len(f.gens)
gens = f.gens + (s,)
if hasattr(f.rep, 'homogenize'):
return f.per(f.rep.homogenize(i), gens=gens)
raise OperationNotSupported(f, 'homogeneous_order')
def homogeneous_order(f):
"""
Returns the homogeneous order of ``f``.
A homogeneous polynomial is a polynomial whose all monomials with
non-zero coefficients have the same total degree. This degree is
the homogeneous order of ``f``. If you only want to check if a
polynomial is homogeneous, then use :func:`Poly.is_homogeneous`.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = Poly(x**5 + 2*x**3*y**2 + 9*x*y**4)
>>> f.homogeneous_order()
5
"""
if hasattr(f.rep, 'homogeneous_order'):
return f.rep.homogeneous_order()
else: # pragma: no cover
raise OperationNotSupported(f, 'homogeneous_order')
def LC(f, order=None):
"""
Returns the leading coefficient of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(4*x**3 + 2*x**2 + 3*x, x).LC()
4
"""
if order is not None:
return f.coeffs(order)[0]
if hasattr(f.rep, 'LC'):
result = f.rep.LC()
else: # pragma: no cover
raise OperationNotSupported(f, 'LC')
return f.rep.dom.to_sympy(result)
def TC(f):
"""
Returns the trailing coefficient of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 + 2*x**2 + 3*x, x).TC()
0
"""
if hasattr(f.rep, 'TC'):
result = f.rep.TC()
else: # pragma: no cover
raise OperationNotSupported(f, 'TC')
return f.rep.dom.to_sympy(result)
def EC(f, order=None):
"""
Returns the last non-zero coefficient of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 + 2*x**2 + 3*x, x).EC()
3
"""
if hasattr(f.rep, 'coeffs'):
return f.coeffs(order)[-1]
else: # pragma: no cover
raise OperationNotSupported(f, 'EC')
def coeff_monomial(f, monom):
"""
Returns the coefficient of ``monom`` in ``f`` if there, else None.
Examples
========
>>> from sympy import Poly, exp
>>> from sympy.abc import x, y
>>> p = Poly(24*x*y*exp(8) + 23*x, x, y)
>>> p.coeff_monomial(x)
23
>>> p.coeff_monomial(y)
0
>>> p.coeff_monomial(x*y)
24*exp(8)
Note that ``Expr.coeff()`` behaves differently, collecting terms
if possible; the Poly must be converted to an Expr to use that
method, however:
>>> p.as_expr().coeff(x)
24*y*exp(8) + 23
>>> p.as_expr().coeff(y)
24*x*exp(8)
>>> p.as_expr().coeff(x*y)
24*exp(8)
See Also
========
nth: more efficient query using exponents of the monomial's generators
"""
return f.nth(*Monomial(monom, f.gens).exponents)
def nth(f, *N):
"""
Returns the ``n``-th coefficient of ``f`` where ``N`` are the
exponents of the generators in the term of interest.
Examples
========
>>> from sympy import Poly, sqrt
>>> from sympy.abc import x, y
>>> Poly(x**3 + 2*x**2 + 3*x, x).nth(2)
2
>>> Poly(x**3 + 2*x*y**2 + y**2, x, y).nth(1, 2)
2
>>> Poly(4*sqrt(x)*y)
Poly(4*y*sqrt(x), y, sqrt(x), domain='ZZ')
>>> _.nth(1, 1)
4
See Also
========
coeff_monomial
"""
if hasattr(f.rep, 'nth'):
if len(N) != len(f.gens):
raise ValueError('exponent of each generator must be specified')
result = f.rep.nth(*list(map(int, N)))
else: # pragma: no cover
raise OperationNotSupported(f, 'nth')
return f.rep.dom.to_sympy(result)
def coeff(f, x, n=1, right=False):
# the semantics of coeff_monomial and Expr.coeff are different;
# if someone is working with a Poly, they should be aware of the
# differences and chose the method best suited for the query.
# Alternatively, a pure-polys method could be written here but
# at this time the ``right`` keyword would be ignored because Poly
# doesn't work with non-commutatives.
raise NotImplementedError(
'Either convert to Expr with `as_expr` method '
'to use Expr\'s coeff method or else use the '
'`coeff_monomial` method of Polys.')
def LM(f, order=None):
"""
Returns the leading monomial of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(4*x**2 + 2*x*y**2 + x*y + 3*y, x, y).LM()
x**2*y**0
"""
return Monomial(f.monoms(order)[0], f.gens)
def EM(f, order=None):
"""
Returns the last non-zero monomial of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(4*x**2 + 2*x*y**2 + x*y + 3*y, x, y).EM()
x**0*y**1
"""
return Monomial(f.monoms(order)[-1], f.gens)
def LT(f, order=None):
"""
Returns the leading term of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(4*x**2 + 2*x*y**2 + x*y + 3*y, x, y).LT()
(x**2*y**0, 4)
"""
monom, coeff = f.terms(order)[0]
return Monomial(monom, f.gens), coeff
def ET(f, order=None):
"""
Returns the last non-zero term of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(4*x**2 + 2*x*y**2 + x*y + 3*y, x, y).ET()
(x**0*y**1, 3)
"""
monom, coeff = f.terms(order)[-1]
return Monomial(monom, f.gens), coeff
def max_norm(f):
"""
Returns maximum norm of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(-x**2 + 2*x - 3, x).max_norm()
3
"""
if hasattr(f.rep, 'max_norm'):
result = f.rep.max_norm()
else: # pragma: no cover
raise OperationNotSupported(f, 'max_norm')
return f.rep.dom.to_sympy(result)
def l1_norm(f):
"""
Returns l1 norm of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(-x**2 + 2*x - 3, x).l1_norm()
6
"""
if hasattr(f.rep, 'l1_norm'):
result = f.rep.l1_norm()
else: # pragma: no cover
raise OperationNotSupported(f, 'l1_norm')
return f.rep.dom.to_sympy(result)
def clear_denoms(self, convert=False):
"""
Clear denominators, but keep the ground domain.
Examples
========
>>> from sympy import Poly, S, QQ
>>> from sympy.abc import x
>>> f = Poly(x/2 + S(1)/3, x, domain=QQ)
>>> f.clear_denoms()
(6, Poly(3*x + 2, x, domain='QQ'))
>>> f.clear_denoms(convert=True)
(6, Poly(3*x + 2, x, domain='ZZ'))
"""
f = self
if not f.rep.dom.has_Field:
return S.One, f
dom = f.get_domain()
if dom.has_assoc_Ring:
dom = f.rep.dom.get_ring()
if hasattr(f.rep, 'clear_denoms'):
coeff, result = f.rep.clear_denoms()
else: # pragma: no cover
raise OperationNotSupported(f, 'clear_denoms')
coeff, f = dom.to_sympy(coeff), f.per(result)
if not convert or not dom.has_assoc_Ring:
return coeff, f
else:
return coeff, f.to_ring()
def rat_clear_denoms(self, g):
"""
Clear denominators in a rational function ``f/g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = Poly(x**2/y + 1, x)
>>> g = Poly(x**3 + y, x)
>>> p, q = f.rat_clear_denoms(g)
>>> p
Poly(x**2 + y, x, domain='ZZ[y]')
>>> q
Poly(y*x**3 + y**2, x, domain='ZZ[y]')
"""
f = self
dom, per, f, g = f._unify(g)
f = per(f)
g = per(g)
if not (dom.has_Field and dom.has_assoc_Ring):
return f, g
a, f = f.clear_denoms(convert=True)
b, g = g.clear_denoms(convert=True)
f = f.mul_ground(b)
g = g.mul_ground(a)
return f, g
def integrate(self, *specs, **args):
"""
Computes indefinite integral of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 2*x + 1, x).integrate()
Poly(1/3*x**3 + x**2 + x, x, domain='QQ')
>>> Poly(x*y**2 + x, x, y).integrate((0, 1), (1, 0))
Poly(1/2*x**2*y**2 + 1/2*x**2, x, y, domain='QQ')
"""
f = self
if args.get('auto', True) and f.rep.dom.has_Ring:
f = f.to_field()
if hasattr(f.rep, 'integrate'):
if not specs:
return f.per(f.rep.integrate(m=1))
rep = f.rep
for spec in specs:
if type(spec) is tuple:
gen, m = spec
else:
gen, m = spec, 1
rep = rep.integrate(int(m), f._gen_to_level(gen))
return f.per(rep)
else: # pragma: no cover
raise OperationNotSupported(f, 'integrate')
def diff(f, *specs):
"""
Computes partial derivative of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + 2*x + 1, x).diff()
Poly(2*x + 2, x, domain='ZZ')
>>> Poly(x*y**2 + x, x, y).diff((0, 0), (1, 1))
Poly(2*x*y, x, y, domain='ZZ')
"""
if hasattr(f.rep, 'diff'):
if not specs:
return f.per(f.rep.diff(m=1))
rep = f.rep
for spec in specs:
if type(spec) is tuple:
gen, m = spec
else:
gen, m = spec, 1
rep = rep.diff(int(m), f._gen_to_level(gen))
return f.per(rep)
else: # pragma: no cover
raise OperationNotSupported(f, 'diff')
def eval(self, x, a=None, auto=True):
"""
Evaluate ``f`` at ``a`` in the given variable.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y, z
>>> Poly(x**2 + 2*x + 3, x).eval(2)
11
>>> Poly(2*x*y + 3*x + y + 2, x, y).eval(x, 2)
Poly(5*y + 8, y, domain='ZZ')
>>> f = Poly(2*x*y + 3*x + y + 2*z, x, y, z)
>>> f.eval({x: 2})
Poly(5*y + 2*z + 6, y, z, domain='ZZ')
>>> f.eval({x: 2, y: 5})
Poly(2*z + 31, z, domain='ZZ')
>>> f.eval({x: 2, y: 5, z: 7})
45
>>> f.eval((2, 5))
Poly(2*z + 31, z, domain='ZZ')
>>> f(2, 5)
Poly(2*z + 31, z, domain='ZZ')
"""
f = self
if a is None:
if isinstance(x, dict):
mapping = x
for gen, value in mapping.items():
f = f.eval(gen, value)
return f
elif isinstance(x, (tuple, list)):
values = x
if len(values) > len(f.gens):
raise ValueError("too many values provided")
for gen, value in zip(f.gens, values):
f = f.eval(gen, value)
return f
else:
j, a = 0, x
else:
j = f._gen_to_level(x)
if not hasattr(f.rep, 'eval'): # pragma: no cover
raise OperationNotSupported(f, 'eval')
try:
result = f.rep.eval(a, j)
except CoercionFailed:
if not auto:
raise DomainError("can't evaluate at %s in %s" % (a, f.rep.dom))
else:
a_domain, [a] = construct_domain([a])
new_domain = f.get_domain().unify_with_symbols(a_domain, f.gens)
f = f.set_domain(new_domain)
a = new_domain.convert(a, a_domain)
result = f.rep.eval(a, j)
return f.per(result, remove=j)
def __call__(f, *values):
"""
Evaluate ``f`` at the give values.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y, z
>>> f = Poly(2*x*y + 3*x + y + 2*z, x, y, z)
>>> f(2)
Poly(5*y + 2*z + 6, y, z, domain='ZZ')
>>> f(2, 5)
Poly(2*z + 31, z, domain='ZZ')
>>> f(2, 5, 7)
45
"""
return f.eval(values)
def half_gcdex(f, g, auto=True):
"""
Half extended Euclidean algorithm of ``f`` and ``g``.
Returns ``(s, h)`` such that ``h = gcd(f, g)`` and ``s*f = h (mod g)``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = x**4 - 2*x**3 - 6*x**2 + 12*x + 15
>>> g = x**3 + x**2 - 4*x - 4
>>> Poly(f).half_gcdex(Poly(g))
(Poly(-1/5*x + 3/5, x, domain='QQ'), Poly(x + 1, x, domain='QQ'))
"""
dom, per, F, G = f._unify(g)
if auto and dom.has_Ring:
F, G = F.to_field(), G.to_field()
if hasattr(f.rep, 'half_gcdex'):
s, h = F.half_gcdex(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'half_gcdex')
return per(s), per(h)
def gcdex(f, g, auto=True):
"""
Extended Euclidean algorithm of ``f`` and ``g``.
Returns ``(s, t, h)`` such that ``h = gcd(f, g)`` and ``s*f + t*g = h``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = x**4 - 2*x**3 - 6*x**2 + 12*x + 15
>>> g = x**3 + x**2 - 4*x - 4
>>> Poly(f).gcdex(Poly(g))
(Poly(-1/5*x + 3/5, x, domain='QQ'),
Poly(1/5*x**2 - 6/5*x + 2, x, domain='QQ'),
Poly(x + 1, x, domain='QQ'))
"""
dom, per, F, G = f._unify(g)
if auto and dom.has_Ring:
F, G = F.to_field(), G.to_field()
if hasattr(f.rep, 'gcdex'):
s, t, h = F.gcdex(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'gcdex')
return per(s), per(t), per(h)
def invert(f, g, auto=True):
"""
Invert ``f`` modulo ``g`` when possible.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).invert(Poly(2*x - 1, x))
Poly(-4/3, x, domain='QQ')
>>> Poly(x**2 - 1, x).invert(Poly(x - 1, x))
Traceback (most recent call last):
...
NotInvertible: zero divisor
"""
dom, per, F, G = f._unify(g)
if auto and dom.has_Ring:
F, G = F.to_field(), G.to_field()
if hasattr(f.rep, 'invert'):
result = F.invert(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'invert')
return per(result)
def revert(f, n):
"""Compute ``f**(-1)`` mod ``x**n``. """
if hasattr(f.rep, 'revert'):
result = f.rep.revert(int(n))
else: # pragma: no cover
raise OperationNotSupported(f, 'revert')
return f.per(result)
def subresultants(f, g):
"""
Computes the subresultant PRS of ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 1, x).subresultants(Poly(x**2 - 1, x))
[Poly(x**2 + 1, x, domain='ZZ'),
Poly(x**2 - 1, x, domain='ZZ'),
Poly(-2, x, domain='ZZ')]
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'subresultants'):
result = F.subresultants(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'subresultants')
return list(map(per, result))
def resultant(f, g, includePRS=False):
"""
Computes the resultant of ``f`` and ``g`` via PRS.
If includePRS=True, it includes the subresultant PRS in the result.
Because the PRS is used to calculate the resultant, this is more
efficient than calling :func:`subresultants` separately.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = Poly(x**2 + 1, x)
>>> f.resultant(Poly(x**2 - 1, x))
4
>>> f.resultant(Poly(x**2 - 1, x), includePRS=True)
(4, [Poly(x**2 + 1, x, domain='ZZ'), Poly(x**2 - 1, x, domain='ZZ'),
Poly(-2, x, domain='ZZ')])
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'resultant'):
if includePRS:
result, R = F.resultant(G, includePRS=includePRS)
else:
result = F.resultant(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'resultant')
if includePRS:
return (per(result, remove=0), list(map(per, R)))
return per(result, remove=0)
def discriminant(f):
"""
Computes the discriminant of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + 2*x + 3, x).discriminant()
-8
"""
if hasattr(f.rep, 'discriminant'):
result = f.rep.discriminant()
else: # pragma: no cover
raise OperationNotSupported(f, 'discriminant')
return f.per(result, remove=0)
def dispersionset(f, g=None):
r"""Compute the *dispersion set* of two polynomials.
For two polynomials `f(x)` and `g(x)` with `\deg f > 0`
and `\deg g > 0` the dispersion set `\operatorname{J}(f, g)` is defined as:
.. math::
\operatorname{J}(f, g)
& := \{a \in \mathbb{N}_0 | \gcd(f(x), g(x+a)) \neq 1\} \\
& = \{a \in \mathbb{N}_0 | \deg \gcd(f(x), g(x+a)) \geq 1\}
For a single polynomial one defines `\operatorname{J}(f) := \operatorname{J}(f, f)`.
Examples
========
>>> from sympy import poly
>>> from sympy.polys.dispersion import dispersion, dispersionset
>>> from sympy.abc import x
Dispersion set and dispersion of a simple polynomial:
>>> fp = poly((x - 3)*(x + 3), x)
>>> sorted(dispersionset(fp))
[0, 6]
>>> dispersion(fp)
6
Note that the definition of the dispersion is not symmetric:
>>> fp = poly(x**4 - 3*x**2 + 1, x)
>>> gp = fp.shift(-3)
>>> sorted(dispersionset(fp, gp))
[2, 3, 4]
>>> dispersion(fp, gp)
4
>>> sorted(dispersionset(gp, fp))
[]
>>> dispersion(gp, fp)
-oo
Computing the dispersion also works over field extensions:
>>> from sympy import sqrt
>>> fp = poly(x**2 + sqrt(5)*x - 1, x, domain='QQ<sqrt(5)>')
>>> gp = poly(x**2 + (2 + sqrt(5))*x + sqrt(5), x, domain='QQ<sqrt(5)>')
>>> sorted(dispersionset(fp, gp))
[2]
>>> sorted(dispersionset(gp, fp))
[1, 4]
We can even perform the computations for polynomials
having symbolic coefficients:
>>> from sympy.abc import a
>>> fp = poly(4*x**4 + (4*a + 8)*x**3 + (a**2 + 6*a + 4)*x**2 + (a**2 + 2*a)*x, x)
>>> sorted(dispersionset(fp))
[0, 1]
See Also
========
dispersion
References
==========
1. [ManWright94]_
2. [Koepf98]_
3. [Abramov71]_
4. [Man93]_
"""
from sympy.polys.dispersion import dispersionset
return dispersionset(f, g)
def dispersion(f, g=None):
r"""Compute the *dispersion* of polynomials.
For two polynomials `f(x)` and `g(x)` with `\deg f > 0`
and `\deg g > 0` the dispersion `\operatorname{dis}(f, g)` is defined as:
.. math::
\operatorname{dis}(f, g)
& := \max\{ J(f,g) \cup \{0\} \} \\
& = \max\{ \{a \in \mathbb{N} | \gcd(f(x), g(x+a)) \neq 1\} \cup \{0\} \}
and for a single polynomial `\operatorname{dis}(f) := \operatorname{dis}(f, f)`.
Examples
========
>>> from sympy import poly
>>> from sympy.polys.dispersion import dispersion, dispersionset
>>> from sympy.abc import x
Dispersion set and dispersion of a simple polynomial:
>>> fp = poly((x - 3)*(x + 3), x)
>>> sorted(dispersionset(fp))
[0, 6]
>>> dispersion(fp)
6
Note that the definition of the dispersion is not symmetric:
>>> fp = poly(x**4 - 3*x**2 + 1, x)
>>> gp = fp.shift(-3)
>>> sorted(dispersionset(fp, gp))
[2, 3, 4]
>>> dispersion(fp, gp)
4
>>> sorted(dispersionset(gp, fp))
[]
>>> dispersion(gp, fp)
-oo
Computing the dispersion also works over field extensions:
>>> from sympy import sqrt
>>> fp = poly(x**2 + sqrt(5)*x - 1, x, domain='QQ<sqrt(5)>')
>>> gp = poly(x**2 + (2 + sqrt(5))*x + sqrt(5), x, domain='QQ<sqrt(5)>')
>>> sorted(dispersionset(fp, gp))
[2]
>>> sorted(dispersionset(gp, fp))
[1, 4]
We can even perform the computations for polynomials
having symbolic coefficients:
>>> from sympy.abc import a
>>> fp = poly(4*x**4 + (4*a + 8)*x**3 + (a**2 + 6*a + 4)*x**2 + (a**2 + 2*a)*x, x)
>>> sorted(dispersionset(fp))
[0, 1]
See Also
========
dispersionset
References
==========
1. [ManWright94]_
2. [Koepf98]_
3. [Abramov71]_
4. [Man93]_
"""
from sympy.polys.dispersion import dispersion
return dispersion(f, g)
def cofactors(f, g):
"""
Returns the GCD of ``f`` and ``g`` and their cofactors.
Returns polynomials ``(h, cff, cfg)`` such that ``h = gcd(f, g)``, and
``cff = quo(f, h)`` and ``cfg = quo(g, h)`` are, so called, cofactors
of ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).cofactors(Poly(x**2 - 3*x + 2, x))
(Poly(x - 1, x, domain='ZZ'),
Poly(x + 1, x, domain='ZZ'),
Poly(x - 2, x, domain='ZZ'))
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'cofactors'):
h, cff, cfg = F.cofactors(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'cofactors')
return per(h), per(cff), per(cfg)
def gcd(f, g):
"""
Returns the polynomial GCD of ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).gcd(Poly(x**2 - 3*x + 2, x))
Poly(x - 1, x, domain='ZZ')
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'gcd'):
result = F.gcd(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'gcd')
return per(result)
def lcm(f, g):
"""
Returns polynomial LCM of ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 1, x).lcm(Poly(x**2 - 3*x + 2, x))
Poly(x**3 - 2*x**2 - x + 2, x, domain='ZZ')
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'lcm'):
result = F.lcm(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'lcm')
return per(result)
def trunc(f, p):
"""
Reduce ``f`` modulo a constant ``p``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x**3 + 3*x**2 + 5*x + 7, x).trunc(3)
Poly(-x**3 - x + 1, x, domain='ZZ')
"""
p = f.rep.dom.convert(p)
if hasattr(f.rep, 'trunc'):
result = f.rep.trunc(p)
else: # pragma: no cover
raise OperationNotSupported(f, 'trunc')
return f.per(result)
def monic(self, auto=True):
"""
Divides all coefficients by ``LC(f)``.
Examples
========
>>> from sympy import Poly, ZZ
>>> from sympy.abc import x
>>> Poly(3*x**2 + 6*x + 9, x, domain=ZZ).monic()
Poly(x**2 + 2*x + 3, x, domain='QQ')
>>> Poly(3*x**2 + 4*x + 2, x, domain=ZZ).monic()
Poly(x**2 + 4/3*x + 2/3, x, domain='QQ')
"""
f = self
if auto and f.rep.dom.has_Ring:
f = f.to_field()
if hasattr(f.rep, 'monic'):
result = f.rep.monic()
else: # pragma: no cover
raise OperationNotSupported(f, 'monic')
return f.per(result)
def content(f):
"""
Returns the GCD of polynomial coefficients.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(6*x**2 + 8*x + 12, x).content()
2
"""
if hasattr(f.rep, 'content'):
result = f.rep.content()
else: # pragma: no cover
raise OperationNotSupported(f, 'content')
return f.rep.dom.to_sympy(result)
def primitive(f):
"""
Returns the content and a primitive form of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x**2 + 8*x + 12, x).primitive()
(2, Poly(x**2 + 4*x + 6, x, domain='ZZ'))
"""
if hasattr(f.rep, 'primitive'):
cont, result = f.rep.primitive()
else: # pragma: no cover
raise OperationNotSupported(f, 'primitive')
return f.rep.dom.to_sympy(cont), f.per(result)
def compose(f, g):
"""
Computes the functional composition of ``f`` and ``g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + x, x).compose(Poly(x - 1, x))
Poly(x**2 - x, x, domain='ZZ')
"""
_, per, F, G = f._unify(g)
if hasattr(f.rep, 'compose'):
result = F.compose(G)
else: # pragma: no cover
raise OperationNotSupported(f, 'compose')
return per(result)
def decompose(f):
"""
Computes a functional decomposition of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**4 + 2*x**3 - x - 1, x, domain='ZZ').decompose()
[Poly(x**2 - x - 1, x, domain='ZZ'), Poly(x**2 + x, x, domain='ZZ')]
"""
if hasattr(f.rep, 'decompose'):
result = f.rep.decompose()
else: # pragma: no cover
raise OperationNotSupported(f, 'decompose')
return list(map(f.per, result))
def shift(f, a):
"""
Efficiently compute Taylor shift ``f(x + a)``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 2*x + 1, x).shift(2)
Poly(x**2 + 2*x + 1, x, domain='ZZ')
"""
if hasattr(f.rep, 'shift'):
result = f.rep.shift(a)
else: # pragma: no cover
raise OperationNotSupported(f, 'shift')
return f.per(result)
def sturm(self, auto=True):
"""
Computes the Sturm sequence of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 - 2*x**2 + x - 3, x).sturm()
[Poly(x**3 - 2*x**2 + x - 3, x, domain='QQ'),
Poly(3*x**2 - 4*x + 1, x, domain='QQ'),
Poly(2/9*x + 25/9, x, domain='QQ'),
Poly(-2079/4, x, domain='QQ')]
"""
f = self
if auto and f.rep.dom.has_Ring:
f = f.to_field()
if hasattr(f.rep, 'sturm'):
result = f.rep.sturm()
else: # pragma: no cover
raise OperationNotSupported(f, 'sturm')
return list(map(f.per, result))
def gff_list(f):
"""
Computes greatest factorial factorization of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = x**5 + 2*x**4 - x**3 - 2*x**2
>>> Poly(f).gff_list()
[(Poly(x, x, domain='ZZ'), 1), (Poly(x + 2, x, domain='ZZ'), 4)]
"""
if hasattr(f.rep, 'gff_list'):
result = f.rep.gff_list()
else: # pragma: no cover
raise OperationNotSupported(f, 'gff_list')
return [(f.per(g), k) for g, k in result]
def sqf_norm(f):
"""
Computes square-free norm of ``f``.
Returns ``s``, ``f``, ``r``, such that ``g(x) = f(x-sa)`` and
``r(x) = Norm(g(x))`` is a square-free polynomial over ``K``,
where ``a`` is the algebraic extension of the ground domain.
Examples
========
>>> from sympy import Poly, sqrt
>>> from sympy.abc import x
>>> s, f, r = Poly(x**2 + 1, x, extension=[sqrt(3)]).sqf_norm()
>>> s
1
>>> f
Poly(x**2 - 2*sqrt(3)*x + 4, x, domain='QQ<sqrt(3)>')
>>> r
Poly(x**4 - 4*x**2 + 16, x, domain='QQ')
"""
if hasattr(f.rep, 'sqf_norm'):
s, g, r = f.rep.sqf_norm()
else: # pragma: no cover
raise OperationNotSupported(f, 'sqf_norm')
return s, f.per(g), f.per(r)
def sqf_part(f):
"""
Computes square-free part of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**3 - 3*x - 2, x).sqf_part()
Poly(x**2 - x - 2, x, domain='ZZ')
"""
if hasattr(f.rep, 'sqf_part'):
result = f.rep.sqf_part()
else: # pragma: no cover
raise OperationNotSupported(f, 'sqf_part')
return f.per(result)
def sqf_list(f, all=False):
"""
Returns a list of square-free factors of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = 2*x**5 + 16*x**4 + 50*x**3 + 76*x**2 + 56*x + 16
>>> Poly(f).sqf_list()
(2, [(Poly(x + 1, x, domain='ZZ'), 2),
(Poly(x + 2, x, domain='ZZ'), 3)])
>>> Poly(f).sqf_list(all=True)
(2, [(Poly(1, x, domain='ZZ'), 1),
(Poly(x + 1, x, domain='ZZ'), 2),
(Poly(x + 2, x, domain='ZZ'), 3)])
"""
if hasattr(f.rep, 'sqf_list'):
coeff, factors = f.rep.sqf_list(all)
else: # pragma: no cover
raise OperationNotSupported(f, 'sqf_list')
return f.rep.dom.to_sympy(coeff), [(f.per(g), k) for g, k in factors]
def sqf_list_include(f, all=False):
"""
Returns a list of square-free factors of ``f``.
Examples
========
>>> from sympy import Poly, expand
>>> from sympy.abc import x
>>> f = expand(2*(x + 1)**3*x**4)
>>> f
2*x**7 + 6*x**6 + 6*x**5 + 2*x**4
>>> Poly(f).sqf_list_include()
[(Poly(2, x, domain='ZZ'), 1),
(Poly(x + 1, x, domain='ZZ'), 3),
(Poly(x, x, domain='ZZ'), 4)]
>>> Poly(f).sqf_list_include(all=True)
[(Poly(2, x, domain='ZZ'), 1),
(Poly(1, x, domain='ZZ'), 2),
(Poly(x + 1, x, domain='ZZ'), 3),
(Poly(x, x, domain='ZZ'), 4)]
"""
if hasattr(f.rep, 'sqf_list_include'):
factors = f.rep.sqf_list_include(all)
else: # pragma: no cover
raise OperationNotSupported(f, 'sqf_list_include')
return [(f.per(g), k) for g, k in factors]
def factor_list(f):
"""
Returns a list of irreducible factors of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = 2*x**5 + 2*x**4*y + 4*x**3 + 4*x**2*y + 2*x + 2*y
>>> Poly(f).factor_list()
(2, [(Poly(x + y, x, y, domain='ZZ'), 1),
(Poly(x**2 + 1, x, y, domain='ZZ'), 2)])
"""
if hasattr(f.rep, 'factor_list'):
try:
coeff, factors = f.rep.factor_list()
except DomainError:
return S.One, [(f, 1)]
else: # pragma: no cover
raise OperationNotSupported(f, 'factor_list')
return f.rep.dom.to_sympy(coeff), [(f.per(g), k) for g, k in factors]
def factor_list_include(f):
"""
Returns a list of irreducible factors of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> f = 2*x**5 + 2*x**4*y + 4*x**3 + 4*x**2*y + 2*x + 2*y
>>> Poly(f).factor_list_include()
[(Poly(2*x + 2*y, x, y, domain='ZZ'), 1),
(Poly(x**2 + 1, x, y, domain='ZZ'), 2)]
"""
if hasattr(f.rep, 'factor_list_include'):
try:
factors = f.rep.factor_list_include()
except DomainError:
return [(f, 1)]
else: # pragma: no cover
raise OperationNotSupported(f, 'factor_list_include')
return [(f.per(g), k) for g, k in factors]
def intervals(f, all=False, eps=None, inf=None, sup=None, fast=False, sqf=False):
"""
Compute isolating intervals for roots of ``f``.
For real roots the Vincent-Akritas-Strzebonski (VAS) continued fractions method is used.
References:
===========
1. Alkiviadis G. Akritas and Adam W. Strzebonski: A Comparative Study of Two Real Root
Isolation Methods . Nonlinear Analysis: Modelling and Control, Vol. 10, No. 4, 297-304, 2005.
2. Alkiviadis G. Akritas, Adam W. Strzebonski and Panagiotis S. Vigklas: Improving the
Performance of the Continued Fractions Method Using new Bounds of Positive Roots. Nonlinear
Analysis: Modelling and Control, Vol. 13, No. 3, 265-279, 2008.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 3, x).intervals()
[((-2, -1), 1), ((1, 2), 1)]
>>> Poly(x**2 - 3, x).intervals(eps=1e-2)
[((-26/15, -19/11), 1), ((19/11, 26/15), 1)]
"""
if eps is not None:
eps = QQ.convert(eps)
if eps <= 0:
raise ValueError("'eps' must be a positive rational")
if inf is not None:
inf = QQ.convert(inf)
if sup is not None:
sup = QQ.convert(sup)
if hasattr(f.rep, 'intervals'):
result = f.rep.intervals(
all=all, eps=eps, inf=inf, sup=sup, fast=fast, sqf=sqf)
else: # pragma: no cover
raise OperationNotSupported(f, 'intervals')
if sqf:
def _real(interval):
s, t = interval
return (QQ.to_sympy(s), QQ.to_sympy(t))
if not all:
return list(map(_real, result))
def _complex(rectangle):
(u, v), (s, t) = rectangle
return (QQ.to_sympy(u) + I*QQ.to_sympy(v),
QQ.to_sympy(s) + I*QQ.to_sympy(t))
real_part, complex_part = result
return list(map(_real, real_part)), list(map(_complex, complex_part))
else:
def _real(interval):
(s, t), k = interval
return ((QQ.to_sympy(s), QQ.to_sympy(t)), k)
if not all:
return list(map(_real, result))
def _complex(rectangle):
((u, v), (s, t)), k = rectangle
return ((QQ.to_sympy(u) + I*QQ.to_sympy(v),
QQ.to_sympy(s) + I*QQ.to_sympy(t)), k)
real_part, complex_part = result
return list(map(_real, real_part)), list(map(_complex, complex_part))
def refine_root(f, s, t, eps=None, steps=None, fast=False, check_sqf=False):
"""
Refine an isolating interval of a root to the given precision.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 3, x).refine_root(1, 2, eps=1e-2)
(19/11, 26/15)
"""
if check_sqf and not f.is_sqf:
raise PolynomialError("only square-free polynomials supported")
s, t = QQ.convert(s), QQ.convert(t)
if eps is not None:
eps = QQ.convert(eps)
if eps <= 0:
raise ValueError("'eps' must be a positive rational")
if steps is not None:
steps = int(steps)
elif eps is None:
steps = 1
if hasattr(f.rep, 'refine_root'):
S, T = f.rep.refine_root(s, t, eps=eps, steps=steps, fast=fast)
else: # pragma: no cover
raise OperationNotSupported(f, 'refine_root')
return QQ.to_sympy(S), QQ.to_sympy(T)
def count_roots(f, inf=None, sup=None):
"""
Return the number of roots of ``f`` in ``[inf, sup]`` interval.
Examples
========
>>> from sympy import Poly, I
>>> from sympy.abc import x
>>> Poly(x**4 - 4, x).count_roots(-3, 3)
2
>>> Poly(x**4 - 4, x).count_roots(0, 1 + 3*I)
1
"""
inf_real, sup_real = True, True
if inf is not None:
inf = sympify(inf)
if inf is S.NegativeInfinity:
inf = None
else:
re, im = inf.as_real_imag()
if not im:
inf = QQ.convert(inf)
else:
inf, inf_real = list(map(QQ.convert, (re, im))), False
if sup is not None:
sup = sympify(sup)
if sup is S.Infinity:
sup = None
else:
re, im = sup.as_real_imag()
if not im:
sup = QQ.convert(sup)
else:
sup, sup_real = list(map(QQ.convert, (re, im))), False
if inf_real and sup_real:
if hasattr(f.rep, 'count_real_roots'):
count = f.rep.count_real_roots(inf=inf, sup=sup)
else: # pragma: no cover
raise OperationNotSupported(f, 'count_real_roots')
else:
if inf_real and inf is not None:
inf = (inf, QQ.zero)
if sup_real and sup is not None:
sup = (sup, QQ.zero)
if hasattr(f.rep, 'count_complex_roots'):
count = f.rep.count_complex_roots(inf=inf, sup=sup)
else: # pragma: no cover
raise OperationNotSupported(f, 'count_complex_roots')
return Integer(count)
def root(f, index, radicals=True):
"""
Get an indexed root of a polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = Poly(2*x**3 - 7*x**2 + 4*x + 4)
>>> f.root(0)
-1/2
>>> f.root(1)
2
>>> f.root(2)
2
>>> f.root(3)
Traceback (most recent call last):
...
IndexError: root index out of [-3, 2] range, got 3
>>> Poly(x**5 + x + 1).root(0)
RootOf(x**3 - x**2 + 1, 0)
"""
return sympy.polys.rootoftools.RootOf(f, index, radicals=radicals)
def real_roots(f, multiple=True, radicals=True):
"""
Return a list of real roots with multiplicities.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x**3 - 7*x**2 + 4*x + 4).real_roots()
[-1/2, 2, 2]
>>> Poly(x**3 + x + 1).real_roots()
[RootOf(x**3 + x + 1, 0)]
"""
reals = sympy.polys.rootoftools.RootOf.real_roots(f, radicals=radicals)
if multiple:
return reals
else:
return group(reals, multiple=False)
def all_roots(f, multiple=True, radicals=True):
"""
Return a list of real and complex roots with multiplicities.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x**3 - 7*x**2 + 4*x + 4).all_roots()
[-1/2, 2, 2]
>>> Poly(x**3 + x + 1).all_roots()
[RootOf(x**3 + x + 1, 0),
RootOf(x**3 + x + 1, 1),
RootOf(x**3 + x + 1, 2)]
"""
roots = sympy.polys.rootoftools.RootOf.all_roots(f, radicals=radicals)
if multiple:
return roots
else:
return group(roots, multiple=False)
def nroots(f, n=15, maxsteps=50, cleanup=True):
"""
Compute numerical approximations of roots of ``f``.
Parameters
==========
n ... the number of digits to calculate
maxsteps ... the maximum number of iterations to do
If the accuracy `n` cannot be reached in `maxsteps`, it will raise an
exception. You need to rerun with higher maxsteps.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 3).nroots(n=15)
[-1.73205080756888, 1.73205080756888]
>>> Poly(x**2 - 3).nroots(n=30)
[-1.73205080756887729352744634151, 1.73205080756887729352744634151]
"""
if f.is_multivariate:
raise MultivariatePolynomialError(
"can't compute numerical roots of %s" % f)
if f.degree() <= 0:
return []
# For integer and rational coefficients, convert them to integers only
# (for accuracy). Otherwise just try to convert the coefficients to
# mpmath.mpc and raise an exception if the conversion fails.
if f.rep.dom is ZZ:
coeffs = [int(coeff) for coeff in f.all_coeffs()]
elif f.rep.dom is QQ:
denoms = [coeff.q for coeff in f.all_coeffs()]
from sympy.core.numbers import ilcm
fac = ilcm(*denoms)
coeffs = [int(coeff*fac) for coeff in f.all_coeffs()]
else:
coeffs = [coeff.evalf(n=n).as_real_imag()
for coeff in f.all_coeffs()]
try:
coeffs = [mpmath.mpc(*coeff) for coeff in coeffs]
except TypeError:
raise DomainError("Numerical domain expected, got %s" % \
f.rep.dom)
dps = mpmath.mp.dps
mpmath.mp.dps = n
try:
# We need to add extra precision to guard against losing accuracy.
# 10 times the degree of the polynomial seems to work well.
roots = mpmath.polyroots(coeffs, maxsteps=maxsteps,
cleanup=cleanup, error=False, extraprec=f.degree()*10)
# Mpmath puts real roots first, then complex ones (as does all_roots)
# so we make sure this convention holds here, too.
roots = list(map(sympify,
sorted(roots, key=lambda r: (1 if r.imag else 0, r.real, r.imag))))
except NoConvergence:
raise NoConvergence(
'convergence to root failed; try n < %s or maxsteps > %s' % (
n, maxsteps))
finally:
mpmath.mp.dps = dps
return roots
def ground_roots(f):
"""
Compute roots of ``f`` by factorization in the ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**6 - 4*x**4 + 4*x**3 - x**2).ground_roots()
{0: 2, 1: 2}
"""
if f.is_multivariate:
raise MultivariatePolynomialError(
"can't compute ground roots of %s" % f)
roots = {}
for factor, k in f.factor_list()[1]:
if factor.is_linear:
a, b = factor.all_coeffs()
roots[-b/a] = k
return roots
def nth_power_roots_poly(f, n):
"""
Construct a polynomial with n-th powers of roots of ``f``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = Poly(x**4 - x**2 + 1)
>>> f.nth_power_roots_poly(2)
Poly(x**4 - 2*x**3 + 3*x**2 - 2*x + 1, x, domain='ZZ')
>>> f.nth_power_roots_poly(3)
Poly(x**4 + 2*x**2 + 1, x, domain='ZZ')
>>> f.nth_power_roots_poly(4)
Poly(x**4 + 2*x**3 + 3*x**2 + 2*x + 1, x, domain='ZZ')
>>> f.nth_power_roots_poly(12)
Poly(x**4 - 4*x**3 + 6*x**2 - 4*x + 1, x, domain='ZZ')
"""
if f.is_multivariate:
raise MultivariatePolynomialError(
"must be a univariate polynomial")
N = sympify(n)
if N.is_Integer and N >= 1:
n = int(N)
else:
raise ValueError("'n' must an integer and n >= 1, got %s" % n)
x = f.gen
t = Dummy('t')
r = f.resultant(f.__class__.from_expr(x**n - t, x, t))
return r.replace(t, x)
def cancel(f, g, include=False):
"""
Cancel common factors in a rational function ``f/g``.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x**2 - 2, x).cancel(Poly(x**2 - 2*x + 1, x))
(1, Poly(2*x + 2, x, domain='ZZ'), Poly(x - 1, x, domain='ZZ'))
>>> Poly(2*x**2 - 2, x).cancel(Poly(x**2 - 2*x + 1, x), include=True)
(Poly(2*x + 2, x, domain='ZZ'), Poly(x - 1, x, domain='ZZ'))
"""
dom, per, F, G = f._unify(g)
if hasattr(F, 'cancel'):
result = F.cancel(G, include=include)
else: # pragma: no cover
raise OperationNotSupported(f, 'cancel')
if not include:
if dom.has_assoc_Ring:
dom = dom.get_ring()
cp, cq, p, q = result
cp = dom.to_sympy(cp)
cq = dom.to_sympy(cq)
return cp/cq, per(p), per(q)
else:
return tuple(map(per, result))
@property
def is_zero(f):
"""
Returns ``True`` if ``f`` is a zero polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(0, x).is_zero
True
>>> Poly(1, x).is_zero
False
"""
return f.rep.is_zero
@property
def is_one(f):
"""
Returns ``True`` if ``f`` is a unit polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(0, x).is_one
False
>>> Poly(1, x).is_one
True
"""
return f.rep.is_one
@property
def is_sqf(f):
"""
Returns ``True`` if ``f`` is a square-free polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 - 2*x + 1, x).is_sqf
False
>>> Poly(x**2 - 1, x).is_sqf
True
"""
return f.rep.is_sqf
@property
def is_monic(f):
"""
Returns ``True`` if the leading coefficient of ``f`` is one.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x + 2, x).is_monic
True
>>> Poly(2*x + 2, x).is_monic
False
"""
return f.rep.is_monic
@property
def is_primitive(f):
"""
Returns ``True`` if GCD of the coefficients of ``f`` is one.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(2*x**2 + 6*x + 12, x).is_primitive
False
>>> Poly(x**2 + 3*x + 6, x).is_primitive
True
"""
return f.rep.is_primitive
@property
def is_ground(f):
"""
Returns ``True`` if ``f`` is an element of the ground domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x, x).is_ground
False
>>> Poly(2, x).is_ground
True
>>> Poly(y, x).is_ground
True
"""
return f.rep.is_ground
@property
def is_linear(f):
"""
Returns ``True`` if ``f`` is linear in all its variables.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x + y + 2, x, y).is_linear
True
>>> Poly(x*y + 2, x, y).is_linear
False
"""
return f.rep.is_linear
@property
def is_quadratic(f):
"""
Returns ``True`` if ``f`` is quadratic in all its variables.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x*y + 2, x, y).is_quadratic
True
>>> Poly(x*y**2 + 2, x, y).is_quadratic
False
"""
return f.rep.is_quadratic
@property
def is_monomial(f):
"""
Returns ``True`` if ``f`` is zero or has only one term.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(3*x**2, x).is_monomial
True
>>> Poly(3*x**2 + 1, x).is_monomial
False
"""
return f.rep.is_monomial
@property
def is_homogeneous(f):
"""
Returns ``True`` if ``f`` is a homogeneous polynomial.
A homogeneous polynomial is a polynomial whose all monomials with
non-zero coefficients have the same total degree. If you want not
only to check if a polynomial is homogeneous but also compute its
homogeneous order, then use :func:`Poly.homogeneous_order`.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + x*y, x, y).is_homogeneous
True
>>> Poly(x**3 + x*y, x, y).is_homogeneous
False
"""
return f.rep.is_homogeneous
@property
def is_irreducible(f):
"""
Returns ``True`` if ``f`` has no factors over its domain.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> Poly(x**2 + x + 1, x, modulus=2).is_irreducible
True
>>> Poly(x**2 + 1, x, modulus=2).is_irreducible
False
"""
return f.rep.is_irreducible
@property
def is_univariate(f):
"""
Returns ``True`` if ``f`` is a univariate polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + x + 1, x).is_univariate
True
>>> Poly(x*y**2 + x*y + 1, x, y).is_univariate
False
>>> Poly(x*y**2 + x*y + 1, x).is_univariate
True
>>> Poly(x**2 + x + 1, x, y).is_univariate
False
"""
return len(f.gens) == 1
@property
def is_multivariate(f):
"""
Returns ``True`` if ``f`` is a multivariate polynomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x, y
>>> Poly(x**2 + x + 1, x).is_multivariate
False
>>> Poly(x*y**2 + x*y + 1, x, y).is_multivariate
True
>>> Poly(x*y**2 + x*y + 1, x).is_multivariate
False
>>> Poly(x**2 + x + 1, x, y).is_multivariate
True
"""
return len(f.gens) != 1
@property
def is_cyclotomic(f):
"""
Returns ``True`` if ``f`` is a cyclotomic polnomial.
Examples
========
>>> from sympy import Poly
>>> from sympy.abc import x
>>> f = x**16 + x**14 - x**10 + x**8 - x**6 + x**2 + 1
>>> Poly(f).is_cyclotomic
False
>>> g = x**16 + x**14 - x**10 - x**8 - x**6 + x**2 + 1
>>> Poly(g).is_cyclotomic
True
"""
return f.rep.is_cyclotomic
def __abs__(f):
return f.abs()
def __neg__(f):
return f.neg()
@_sympifyit('g', NotImplemented)
def __add__(f, g):
if not g.is_Poly:
try:
g = f.__class__(g, *f.gens)
except PolynomialError:
return f.as_expr() + g
return f.add(g)
@_sympifyit('g', NotImplemented)
def __radd__(f, g):
if not g.is_Poly:
try:
g = f.__class__(g, *f.gens)
except PolynomialError:
return g + f.as_expr()
return g.add(f)
@_sympifyit('g', NotImplemented)
def __sub__(f, g):
if not g.is_Poly:
try:
g = f.__class__(g, *f.gens)
except PolynomialError:
return f.as_expr() - g
return f.sub(g)
@_sympifyit('g', NotImplemented)
def __rsub__(f, g):
if not g.is_Poly:
try:
g = f.__class__(g, *f.gens)
except PolynomialError:
return g - f.as_expr()
return g.sub(f)
@_sympifyit('g', NotImplemented)
def __mul__(f, g):
if not g.is_Poly:
try:
g = f.__class__(g, *f.gens)
except PolynomialError:
return f.as_expr()*g
return f.mul(g)
@_sympifyit('g', NotImplemented)
def __rmul__(f, g):
if not g.is_Poly:
try:
g = f.__class__(g, *f.gens)
except PolynomialError:
return g*f.as_expr()
return g.mul(f)
@_sympifyit('n', NotImplemented)
def __pow__(f, n):
if n.is_Integer and n >= 0:
return f.pow(n)
else:
return f.as_expr()**n
@_sympifyit('g', NotImplemented)
def __divmod__(f, g):
if not g.is_Poly:
g = f.__class__(g, *f.gens)
return f.div(g)
@_sympifyit('g', NotImplemented)
def __rdivmod__(f, g):
if not g.is_Poly:
g = f.__class__(g, *f.gens)
return g.div(f)
@_sympifyit('g', NotImplemented)
def __mod__(f, g):
if not g.is_Poly:
g = f.__class__(g, *f.gens)
return f.rem(g)
@_sympifyit('g', NotImplemented)
def __rmod__(f, g):
if not g.is_Poly:
g = f.__class__(g, *f.gens)
return g.rem(f)
@_sympifyit('g', NotImplemented)
def __floordiv__(f, g):
if not g.is_Poly:
g = f.__class__(g, *f.gens)
return f.quo(g)
@_sympifyit('g', NotImplemented)
def __rfloordiv__(f, g):
if not g.is_Poly:
g = f.__class__(g, *f.gens)
return g.quo(f)
@_sympifyit('g', NotImplemented)
def __div__(f, g):
return f.as_expr()/g.as_expr()
@_sympifyit('g', NotImplemented)
def __rdiv__(f, g):
return g.as_expr()/f.as_expr()
__truediv__ = __div__
__rtruediv__ = __rdiv__
@_sympifyit('other', NotImplemented)
def __eq__(self, other):
f, g = self, other
if not g.is_Poly:
try:
g = f.__class__(g, f.gens, domain=f.get_domain())
except (PolynomialError, DomainError, CoercionFailed):
return False
if f.gens != g.gens:
return False
if f.rep.dom != g.rep.dom:
try:
dom = f.rep.dom.unify(g.rep.dom, f.gens)
except UnificationFailed:
return False
f = f.set_domain(dom)
g = g.set_domain(dom)
return f.rep == g.rep
@_sympifyit('g', NotImplemented)
def __ne__(f, g):
return not f.__eq__(g)
def __nonzero__(f):
return not f.is_zero
__bool__ = __nonzero__
def eq(f, g, strict=False):
if not strict:
return f.__eq__(g)
else:
return f._strict_eq(sympify(g))
def ne(f, g, strict=False):
return not f.eq(g, strict=strict)
def _strict_eq(f, g):
return isinstance(g, f.__class__) and f.gens == g.gens and f.rep.eq(g.rep, strict=True)
@public
class PurePoly(Poly):
"""Class for representing pure polynomials. """
def _hashable_content(self):
"""Allow SymPy to hash Poly instances. """
return (self.rep,)
def __hash__(self):
return super(PurePoly, self).__hash__()
@property
def free_symbols(self):
"""
Free symbols of a polynomial.
Examples
========
>>> from sympy import PurePoly
>>> from sympy.abc import x, y
>>> PurePoly(x**2 + 1).free_symbols
set()
>>> PurePoly(x**2 + y).free_symbols
set()
>>> PurePoly(x**2 + y, x).free_symbols
set([y])
"""
return self.free_symbols_in_domain
@_sympifyit('other', NotImplemented)
def __eq__(self, other):
f, g = self, other
if not g.is_Poly:
try:
g = f.__class__(g, f.gens, domain=f.get_domain())
except (PolynomialError, DomainError, CoercionFailed):
return False
if len(f.gens) != len(g.gens):
return False
if f.rep.dom != g.rep.dom:
try:
dom = f.rep.dom.unify(g.rep.dom, f.gens)
except UnificationFailed:
return False
f = f.set_domain(dom)
g = g.set_domain(dom)
return f.rep == g.rep
def _strict_eq(f, g):
return isinstance(g, f.__class__) and f.rep.eq(g.rep, strict=True)
def _unify(f, g):
g = sympify(g)
if not g.is_Poly:
try:
return f.rep.dom, f.per, f.rep, f.rep.per(f.rep.dom.from_sympy(g))
except CoercionFailed:
raise UnificationFailed("can't unify %s with %s" % (f, g))
if len(f.gens) != len(g.gens):
raise UnificationFailed("can't unify %s with %s" % (f, g))
if not (isinstance(f.rep, DMP) and isinstance(g.rep, DMP)):
raise UnificationFailed("can't unify %s with %s" % (f, g))
cls = f.__class__
gens = f.gens
dom = f.rep.dom.unify(g.rep.dom, gens)
F = f.rep.convert(dom)
G = g.rep.convert(dom)
def per(rep, dom=dom, gens=gens, remove=None):
if remove is not None:
gens = gens[:remove] + gens[remove + 1:]
if not gens:
return dom.to_sympy(rep)
return cls.new(rep, *gens)
return dom, per, F, G
@public
def poly_from_expr(expr, *gens, **args):
"""Construct a polynomial from an expression. """
opt = options.build_options(gens, args)
return _poly_from_expr(expr, opt)
def _poly_from_expr(expr, opt):
"""Construct a polynomial from an expression. """
orig, expr = expr, sympify(expr)
if not isinstance(expr, Basic):
raise PolificationFailed(opt, orig, expr)
elif expr.is_Poly:
poly = expr.__class__._from_poly(expr, opt)
opt.gens = poly.gens
opt.domain = poly.domain
if opt.polys is None:
opt.polys = True
return poly, opt
elif opt.expand:
expr = expr.expand()
try:
rep, opt = _dict_from_expr(expr, opt)
except GeneratorsNeeded:
raise PolificationFailed(opt, orig, expr)
monoms, coeffs = list(zip(*list(rep.items())))
domain = opt.domain
if domain is None:
opt.domain, coeffs = construct_domain(coeffs, opt=opt)
else:
coeffs = list(map(domain.from_sympy, coeffs))
rep = dict(list(zip(monoms, coeffs)))
poly = Poly._from_dict(rep, opt)
if opt.polys is None:
opt.polys = False
return poly, opt
@public
def parallel_poly_from_expr(exprs, *gens, **args):
"""Construct polynomials from expressions. """
opt = options.build_options(gens, args)
return _parallel_poly_from_expr(exprs, opt)
def _parallel_poly_from_expr(exprs, opt):
"""Construct polynomials from expressions. """
from sympy.functions.elementary.piecewise import Piecewise
if len(exprs) == 2:
f, g = exprs
if isinstance(f, Poly) and isinstance(g, Poly):
f = f.__class__._from_poly(f, opt)
g = g.__class__._from_poly(g, opt)
f, g = f.unify(g)
opt.gens = f.gens
opt.domain = f.domain
if opt.polys is None:
opt.polys = True
return [f, g], opt
origs, exprs = list(exprs), []
_exprs, _polys = [], []
failed = False
for i, expr in enumerate(origs):
expr = sympify(expr)
if isinstance(expr, Basic):
if expr.is_Poly:
_polys.append(i)
else:
_exprs.append(i)
if opt.expand:
expr = expr.expand()
else:
failed = True
exprs.append(expr)
if failed:
raise PolificationFailed(opt, origs, exprs, True)
if _polys:
# XXX: this is a temporary solution
for i in _polys:
exprs[i] = exprs[i].as_expr()
try:
reps, opt = _parallel_dict_from_expr(exprs, opt)
except GeneratorsNeeded:
raise PolificationFailed(opt, origs, exprs, True)
for k in opt.gens:
if isinstance(k, Piecewise):
raise PolynomialError("Piecewise generators do not make sense")
coeffs_list, lengths = [], []
all_monoms = []
all_coeffs = []
for rep in reps:
monoms, coeffs = list(zip(*list(rep.items())))
coeffs_list.extend(coeffs)
all_monoms.append(monoms)
lengths.append(len(coeffs))
domain = opt.domain
if domain is None:
opt.domain, coeffs_list = construct_domain(coeffs_list, opt=opt)
else:
coeffs_list = list(map(domain.from_sympy, coeffs_list))
for k in lengths:
all_coeffs.append(coeffs_list[:k])
coeffs_list = coeffs_list[k:]
polys = []
for monoms, coeffs in zip(all_monoms, all_coeffs):
rep = dict(list(zip(monoms, coeffs)))
poly = Poly._from_dict(rep, opt)
polys.append(poly)
if opt.polys is None:
opt.polys = bool(_polys)
return polys, opt
def _update_args(args, key, value):
"""Add a new ``(key, value)`` pair to arguments ``dict``. """
args = dict(args)
if key not in args:
args[key] = value
return args
@public
def degree(f, *gens, **args):
"""
Return the degree of ``f`` in the given variable.
The degree of 0 is negative infinity.
Examples
========
>>> from sympy import degree
>>> from sympy.abc import x, y
>>> degree(x**2 + y*x + 1, gen=x)
2
>>> degree(x**2 + y*x + 1, gen=y)
1
>>> degree(0, x)
-oo
"""
options.allowed_flags(args, ['gen', 'polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('degree', 1, exc)
return sympify(F.degree(opt.gen))
@public
def degree_list(f, *gens, **args):
"""
Return a list of degrees of ``f`` in all variables.
Examples
========
>>> from sympy import degree_list
>>> from sympy.abc import x, y
>>> degree_list(x**2 + y*x + 1)
(2, 1)
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('degree_list', 1, exc)
degrees = F.degree_list()
return tuple(map(Integer, degrees))
@public
def LC(f, *gens, **args):
"""
Return the leading coefficient of ``f``.
Examples
========
>>> from sympy import LC
>>> from sympy.abc import x, y
>>> LC(4*x**2 + 2*x*y**2 + x*y + 3*y)
4
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('LC', 1, exc)
return F.LC(order=opt.order)
@public
def LM(f, *gens, **args):
"""
Return the leading monomial of ``f``.
Examples
========
>>> from sympy import LM
>>> from sympy.abc import x, y
>>> LM(4*x**2 + 2*x*y**2 + x*y + 3*y)
x**2
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('LM', 1, exc)
monom = F.LM(order=opt.order)
return monom.as_expr()
@public
def LT(f, *gens, **args):
"""
Return the leading term of ``f``.
Examples
========
>>> from sympy import LT
>>> from sympy.abc import x, y
>>> LT(4*x**2 + 2*x*y**2 + x*y + 3*y)
4*x**2
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('LT', 1, exc)
monom, coeff = F.LT(order=opt.order)
return coeff*monom.as_expr()
@public
def pdiv(f, g, *gens, **args):
"""
Compute polynomial pseudo-division of ``f`` and ``g``.
Examples
========
>>> from sympy import pdiv
>>> from sympy.abc import x
>>> pdiv(x**2 + 1, 2*x - 4)
(2*x + 4, 20)
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('pdiv', 2, exc)
q, r = F.pdiv(G)
if not opt.polys:
return q.as_expr(), r.as_expr()
else:
return q, r
@public
def prem(f, g, *gens, **args):
"""
Compute polynomial pseudo-remainder of ``f`` and ``g``.
Examples
========
>>> from sympy import prem
>>> from sympy.abc import x
>>> prem(x**2 + 1, 2*x - 4)
20
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('prem', 2, exc)
r = F.prem(G)
if not opt.polys:
return r.as_expr()
else:
return r
@public
def pquo(f, g, *gens, **args):
"""
Compute polynomial pseudo-quotient of ``f`` and ``g``.
Examples
========
>>> from sympy import pquo
>>> from sympy.abc import x
>>> pquo(x**2 + 1, 2*x - 4)
2*x + 4
>>> pquo(x**2 - 1, 2*x - 1)
2*x + 1
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('pquo', 2, exc)
try:
q = F.pquo(G)
except ExactQuotientFailed:
raise ExactQuotientFailed(f, g)
if not opt.polys:
return q.as_expr()
else:
return q
@public
def pexquo(f, g, *gens, **args):
"""
Compute polynomial exact pseudo-quotient of ``f`` and ``g``.
Examples
========
>>> from sympy import pexquo
>>> from sympy.abc import x
>>> pexquo(x**2 - 1, 2*x - 2)
2*x + 2
>>> pexquo(x**2 + 1, 2*x - 4)
Traceback (most recent call last):
...
ExactQuotientFailed: 2*x - 4 does not divide x**2 + 1
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('pexquo', 2, exc)
q = F.pexquo(G)
if not opt.polys:
return q.as_expr()
else:
return q
@public
def div(f, g, *gens, **args):
"""
Compute polynomial division of ``f`` and ``g``.
Examples
========
>>> from sympy import div, ZZ, QQ
>>> from sympy.abc import x
>>> div(x**2 + 1, 2*x - 4, domain=ZZ)
(0, x**2 + 1)
>>> div(x**2 + 1, 2*x - 4, domain=QQ)
(x/2 + 1, 5)
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('div', 2, exc)
q, r = F.div(G, auto=opt.auto)
if not opt.polys:
return q.as_expr(), r.as_expr()
else:
return q, r
@public
def rem(f, g, *gens, **args):
"""
Compute polynomial remainder of ``f`` and ``g``.
Examples
========
>>> from sympy import rem, ZZ, QQ
>>> from sympy.abc import x
>>> rem(x**2 + 1, 2*x - 4, domain=ZZ)
x**2 + 1
>>> rem(x**2 + 1, 2*x - 4, domain=QQ)
5
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('rem', 2, exc)
r = F.rem(G, auto=opt.auto)
if not opt.polys:
return r.as_expr()
else:
return r
@public
def quo(f, g, *gens, **args):
"""
Compute polynomial quotient of ``f`` and ``g``.
Examples
========
>>> from sympy import quo
>>> from sympy.abc import x
>>> quo(x**2 + 1, 2*x - 4)
x/2 + 1
>>> quo(x**2 - 1, x - 1)
x + 1
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('quo', 2, exc)
q = F.quo(G, auto=opt.auto)
if not opt.polys:
return q.as_expr()
else:
return q
@public
def exquo(f, g, *gens, **args):
"""
Compute polynomial exact quotient of ``f`` and ``g``.
Examples
========
>>> from sympy import exquo
>>> from sympy.abc import x
>>> exquo(x**2 - 1, x - 1)
x + 1
>>> exquo(x**2 + 1, 2*x - 4)
Traceback (most recent call last):
...
ExactQuotientFailed: 2*x - 4 does not divide x**2 + 1
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('exquo', 2, exc)
q = F.exquo(G, auto=opt.auto)
if not opt.polys:
return q.as_expr()
else:
return q
@public
def half_gcdex(f, g, *gens, **args):
"""
Half extended Euclidean algorithm of ``f`` and ``g``.
Returns ``(s, h)`` such that ``h = gcd(f, g)`` and ``s*f = h (mod g)``.
Examples
========
>>> from sympy import half_gcdex
>>> from sympy.abc import x
>>> half_gcdex(x**4 - 2*x**3 - 6*x**2 + 12*x + 15, x**3 + x**2 - 4*x - 4)
(-x/5 + 3/5, x + 1)
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
domain, (a, b) = construct_domain(exc.exprs)
try:
s, h = domain.half_gcdex(a, b)
except NotImplementedError:
raise ComputationFailed('half_gcdex', 2, exc)
else:
return domain.to_sympy(s), domain.to_sympy(h)
s, h = F.half_gcdex(G, auto=opt.auto)
if not opt.polys:
return s.as_expr(), h.as_expr()
else:
return s, h
@public
def gcdex(f, g, *gens, **args):
"""
Extended Euclidean algorithm of ``f`` and ``g``.
Returns ``(s, t, h)`` such that ``h = gcd(f, g)`` and ``s*f + t*g = h``.
Examples
========
>>> from sympy import gcdex
>>> from sympy.abc import x
>>> gcdex(x**4 - 2*x**3 - 6*x**2 + 12*x + 15, x**3 + x**2 - 4*x - 4)
(-x/5 + 3/5, x**2/5 - 6*x/5 + 2, x + 1)
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
domain, (a, b) = construct_domain(exc.exprs)
try:
s, t, h = domain.gcdex(a, b)
except NotImplementedError:
raise ComputationFailed('gcdex', 2, exc)
else:
return domain.to_sympy(s), domain.to_sympy(t), domain.to_sympy(h)
s, t, h = F.gcdex(G, auto=opt.auto)
if not opt.polys:
return s.as_expr(), t.as_expr(), h.as_expr()
else:
return s, t, h
@public
def invert(f, g, *gens, **args):
"""
Invert ``f`` modulo ``g`` when possible.
Examples
========
>>> from sympy import invert
>>> from sympy.abc import x
>>> invert(x**2 - 1, 2*x - 1)
-4/3
>>> invert(x**2 - 1, x - 1)
Traceback (most recent call last):
...
NotInvertible: zero divisor
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
domain, (a, b) = construct_domain(exc.exprs)
try:
return domain.to_sympy(domain.invert(a, b))
except NotImplementedError:
raise ComputationFailed('invert', 2, exc)
h = F.invert(G, auto=opt.auto)
if not opt.polys:
return h.as_expr()
else:
return h
@public
def subresultants(f, g, *gens, **args):
"""
Compute subresultant PRS of ``f`` and ``g``.
Examples
========
>>> from sympy import subresultants
>>> from sympy.abc import x
>>> subresultants(x**2 + 1, x**2 - 1)
[x**2 + 1, x**2 - 1, -2]
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('subresultants', 2, exc)
result = F.subresultants(G)
if not opt.polys:
return [r.as_expr() for r in result]
else:
return result
@public
def resultant(f, g, *gens, **args):
"""
Compute resultant of ``f`` and ``g``.
Examples
========
>>> from sympy import resultant
>>> from sympy.abc import x
>>> resultant(x**2 + 1, x**2 - 1)
4
"""
includePRS = args.pop('includePRS', False)
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('resultant', 2, exc)
if includePRS:
result, R = F.resultant(G, includePRS=includePRS)
else:
result = F.resultant(G)
if not opt.polys:
if includePRS:
return result.as_expr(), [r.as_expr() for r in R]
return result.as_expr()
else:
if includePRS:
return result, R
return result
@public
def discriminant(f, *gens, **args):
"""
Compute discriminant of ``f``.
Examples
========
>>> from sympy import discriminant
>>> from sympy.abc import x
>>> discriminant(x**2 + 2*x + 3)
-8
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('discriminant', 1, exc)
result = F.discriminant()
if not opt.polys:
return result.as_expr()
else:
return result
@public
def cofactors(f, g, *gens, **args):
"""
Compute GCD and cofactors of ``f`` and ``g``.
Returns polynomials ``(h, cff, cfg)`` such that ``h = gcd(f, g)``, and
``cff = quo(f, h)`` and ``cfg = quo(g, h)`` are, so called, cofactors
of ``f`` and ``g``.
Examples
========
>>> from sympy import cofactors
>>> from sympy.abc import x
>>> cofactors(x**2 - 1, x**2 - 3*x + 2)
(x - 1, x + 1, x - 2)
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
domain, (a, b) = construct_domain(exc.exprs)
try:
h, cff, cfg = domain.cofactors(a, b)
except NotImplementedError:
raise ComputationFailed('cofactors', 2, exc)
else:
return domain.to_sympy(h), domain.to_sympy(cff), domain.to_sympy(cfg)
h, cff, cfg = F.cofactors(G)
if not opt.polys:
return h.as_expr(), cff.as_expr(), cfg.as_expr()
else:
return h, cff, cfg
@public
def gcd_list(seq, *gens, **args):
"""
Compute GCD of a list of polynomials.
Examples
========
>>> from sympy import gcd_list
>>> from sympy.abc import x
>>> gcd_list([x**3 - 1, x**2 - 1, x**2 - 3*x + 2])
x - 1
"""
seq = sympify(seq)
def try_non_polynomial_gcd(seq):
if not gens and not args:
domain, numbers = construct_domain(seq)
if not numbers:
return domain.zero
elif domain.is_Numerical:
result, numbers = numbers[0], numbers[1:]
for number in numbers:
result = domain.gcd(result, number)
if domain.is_one(result):
break
return domain.to_sympy(result)
return None
result = try_non_polynomial_gcd(seq)
if result is not None:
return result
options.allowed_flags(args, ['polys'])
try:
polys, opt = parallel_poly_from_expr(seq, *gens, **args)
except PolificationFailed as exc:
result = try_non_polynomial_gcd(exc.exprs)
if result is not None:
return result
else:
raise ComputationFailed('gcd_list', len(seq), exc)
if not polys:
if not opt.polys:
return S.Zero
else:
return Poly(0, opt=opt)
result, polys = polys[0], polys[1:]
for poly in polys:
result = result.gcd(poly)
if result.is_one:
break
if not opt.polys:
return result.as_expr()
else:
return result
@public
def gcd(f, g=None, *gens, **args):
"""
Compute GCD of ``f`` and ``g``.
Examples
========
>>> from sympy import gcd
>>> from sympy.abc import x
>>> gcd(x**2 - 1, x**2 - 3*x + 2)
x - 1
"""
if hasattr(f, '__iter__'):
if g is not None:
gens = (g,) + gens
return gcd_list(f, *gens, **args)
elif g is None:
raise TypeError("gcd() takes 2 arguments or a sequence of arguments")
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
domain, (a, b) = construct_domain(exc.exprs)
try:
return domain.to_sympy(domain.gcd(a, b))
except NotImplementedError:
raise ComputationFailed('gcd', 2, exc)
result = F.gcd(G)
if not opt.polys:
return result.as_expr()
else:
return result
@public
def lcm_list(seq, *gens, **args):
"""
Compute LCM of a list of polynomials.
Examples
========
>>> from sympy import lcm_list
>>> from sympy.abc import x
>>> lcm_list([x**3 - 1, x**2 - 1, x**2 - 3*x + 2])
x**5 - x**4 - 2*x**3 - x**2 + x + 2
"""
seq = sympify(seq)
def try_non_polynomial_lcm(seq):
if not gens and not args:
domain, numbers = construct_domain(seq)
if not numbers:
return domain.one
elif domain.is_Numerical:
result, numbers = numbers[0], numbers[1:]
for number in numbers:
result = domain.lcm(result, number)
return domain.to_sympy(result)
return None
result = try_non_polynomial_lcm(seq)
if result is not None:
return result
options.allowed_flags(args, ['polys'])
try:
polys, opt = parallel_poly_from_expr(seq, *gens, **args)
except PolificationFailed as exc:
result = try_non_polynomial_lcm(exc.exprs)
if result is not None:
return result
else:
raise ComputationFailed('lcm_list', len(seq), exc)
if not polys:
if not opt.polys:
return S.One
else:
return Poly(1, opt=opt)
result, polys = polys[0], polys[1:]
for poly in polys:
result = result.lcm(poly)
if not opt.polys:
return result.as_expr()
else:
return result
@public
def lcm(f, g=None, *gens, **args):
"""
Compute LCM of ``f`` and ``g``.
Examples
========
>>> from sympy import lcm
>>> from sympy.abc import x
>>> lcm(x**2 - 1, x**2 - 3*x + 2)
x**3 - 2*x**2 - x + 2
"""
if hasattr(f, '__iter__'):
if g is not None:
gens = (g,) + gens
return lcm_list(f, *gens, **args)
elif g is None:
raise TypeError("lcm() takes 2 arguments or a sequence of arguments")
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
domain, (a, b) = construct_domain(exc.exprs)
try:
return domain.to_sympy(domain.lcm(a, b))
except NotImplementedError:
raise ComputationFailed('lcm', 2, exc)
result = F.lcm(G)
if not opt.polys:
return result.as_expr()
else:
return result
@public
def terms_gcd(f, *gens, **args):
"""
Remove GCD of terms from ``f``.
If the ``deep`` flag is True, then the arguments of ``f`` will have
terms_gcd applied to them.
If a fraction is factored out of ``f`` and ``f`` is an Add, then
an unevaluated Mul will be returned so that automatic simplification
does not redistribute it. The hint ``clear``, when set to False, can be
used to prevent such factoring when all coefficients are not fractions.
Examples
========
>>> from sympy import terms_gcd, cos
>>> from sympy.abc import x, y
>>> terms_gcd(x**6*y**2 + x**3*y, x, y)
x**3*y*(x**3*y + 1)
The default action of polys routines is to expand the expression
given to them. terms_gcd follows this behavior:
>>> terms_gcd((3+3*x)*(x+x*y))
3*x*(x*y + x + y + 1)
If this is not desired then the hint ``expand`` can be set to False.
In this case the expression will be treated as though it were comprised
of one or more terms:
>>> terms_gcd((3+3*x)*(x+x*y), expand=False)
(3*x + 3)*(x*y + x)
In order to traverse factors of a Mul or the arguments of other
functions, the ``deep`` hint can be used:
>>> terms_gcd((3 + 3*x)*(x + x*y), expand=False, deep=True)
3*x*(x + 1)*(y + 1)
>>> terms_gcd(cos(x + x*y), deep=True)
cos(x*(y + 1))
Rationals are factored out by default:
>>> terms_gcd(x + y/2)
(2*x + y)/2
Only the y-term had a coefficient that was a fraction; if one
does not want to factor out the 1/2 in cases like this, the
flag ``clear`` can be set to False:
>>> terms_gcd(x + y/2, clear=False)
x + y/2
>>> terms_gcd(x*y/2 + y**2, clear=False)
y*(x/2 + y)
The ``clear`` flag is ignored if all coefficients are fractions:
>>> terms_gcd(x/3 + y/2, clear=False)
(2*x + 3*y)/6
See Also
========
sympy.core.exprtools.gcd_terms, sympy.core.exprtools.factor_terms
"""
from sympy.core.relational import Equality
orig = sympify(f)
if not isinstance(f, Expr) or f.is_Atom:
return orig
if args.get('deep', False):
new = f.func(*[terms_gcd(a, *gens, **args) for a in f.args])
args.pop('deep')
args['expand'] = False
return terms_gcd(new, *gens, **args)
if isinstance(f, Equality):
return f
clear = args.pop('clear', True)
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
return exc.expr
J, f = F.terms_gcd()
if opt.domain.has_Ring:
if opt.domain.has_Field:
denom, f = f.clear_denoms(convert=True)
coeff, f = f.primitive()
if opt.domain.has_Field:
coeff /= denom
else:
coeff = S.One
term = Mul(*[x**j for x, j in zip(f.gens, J)])
if coeff == 1:
coeff = S.One
if term == 1:
return orig
if clear:
return _keep_coeff(coeff, term*f.as_expr())
# base the clearing on the form of the original expression, not
# the (perhaps) Mul that we have now
coeff, f = _keep_coeff(coeff, f.as_expr(), clear=False).as_coeff_Mul()
return _keep_coeff(coeff, term*f, clear=False)
@public
def trunc(f, p, *gens, **args):
"""
Reduce ``f`` modulo a constant ``p``.
Examples
========
>>> from sympy import trunc
>>> from sympy.abc import x
>>> trunc(2*x**3 + 3*x**2 + 5*x + 7, 3)
-x**3 - x + 1
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('trunc', 1, exc)
result = F.trunc(sympify(p))
if not opt.polys:
return result.as_expr()
else:
return result
@public
def monic(f, *gens, **args):
"""
Divide all coefficients of ``f`` by ``LC(f)``.
Examples
========
>>> from sympy import monic
>>> from sympy.abc import x
>>> monic(3*x**2 + 4*x + 2)
x**2 + 4*x/3 + 2/3
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('monic', 1, exc)
result = F.monic(auto=opt.auto)
if not opt.polys:
return result.as_expr()
else:
return result
@public
def content(f, *gens, **args):
"""
Compute GCD of coefficients of ``f``.
Examples
========
>>> from sympy import content
>>> from sympy.abc import x
>>> content(6*x**2 + 8*x + 12)
2
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('content', 1, exc)
return F.content()
@public
def primitive(f, *gens, **args):
"""
Compute content and the primitive form of ``f``.
Examples
========
>>> from sympy.polys.polytools import primitive
>>> from sympy.abc import x
>>> primitive(6*x**2 + 8*x + 12)
(2, 3*x**2 + 4*x + 6)
>>> eq = (2 + 2*x)*x + 2
Expansion is performed by default:
>>> primitive(eq)
(2, x**2 + x + 1)
Set ``expand`` to False to shut this off. Note that the
extraction will not be recursive; use the as_content_primitive method
for recursive, non-destructive Rational extraction.
>>> primitive(eq, expand=False)
(1, x*(2*x + 2) + 2)
>>> eq.as_content_primitive()
(2, x*(x + 1) + 1)
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('primitive', 1, exc)
cont, result = F.primitive()
if not opt.polys:
return cont, result.as_expr()
else:
return cont, result
@public
def compose(f, g, *gens, **args):
"""
Compute functional composition ``f(g)``.
Examples
========
>>> from sympy import compose
>>> from sympy.abc import x
>>> compose(x**2 + x, x - 1)
x**2 - x
"""
options.allowed_flags(args, ['polys'])
try:
(F, G), opt = parallel_poly_from_expr((f, g), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('compose', 2, exc)
result = F.compose(G)
if not opt.polys:
return result.as_expr()
else:
return result
@public
def decompose(f, *gens, **args):
"""
Compute functional decomposition of ``f``.
Examples
========
>>> from sympy import decompose
>>> from sympy.abc import x
>>> decompose(x**4 + 2*x**3 - x - 1)
[x**2 - x - 1, x**2 + x]
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('decompose', 1, exc)
result = F.decompose()
if not opt.polys:
return [r.as_expr() for r in result]
else:
return result
@public
def sturm(f, *gens, **args):
"""
Compute Sturm sequence of ``f``.
Examples
========
>>> from sympy import sturm
>>> from sympy.abc import x
>>> sturm(x**3 - 2*x**2 + x - 3)
[x**3 - 2*x**2 + x - 3, 3*x**2 - 4*x + 1, 2*x/9 + 25/9, -2079/4]
"""
options.allowed_flags(args, ['auto', 'polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('sturm', 1, exc)
result = F.sturm(auto=opt.auto)
if not opt.polys:
return [r.as_expr() for r in result]
else:
return result
@public
def gff_list(f, *gens, **args):
"""
Compute a list of greatest factorial factors of ``f``.
Examples
========
>>> from sympy import gff_list, ff
>>> from sympy.abc import x
>>> f = x**5 + 2*x**4 - x**3 - 2*x**2
>>> gff_list(f)
[(x, 1), (x + 2, 4)]
>>> (ff(x, 1)*ff(x + 2, 4)).expand() == f
True
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('gff_list', 1, exc)
factors = F.gff_list()
if not opt.polys:
return [(g.as_expr(), k) for g, k in factors]
else:
return factors
@public
def gff(f, *gens, **args):
"""Compute greatest factorial factorization of ``f``. """
raise NotImplementedError('symbolic falling factorial')
@public
def sqf_norm(f, *gens, **args):
"""
Compute square-free norm of ``f``.
Returns ``s``, ``f``, ``r``, such that ``g(x) = f(x-sa)`` and
``r(x) = Norm(g(x))`` is a square-free polynomial over ``K``,
where ``a`` is the algebraic extension of the ground domain.
Examples
========
>>> from sympy import sqf_norm, sqrt
>>> from sympy.abc import x
>>> sqf_norm(x**2 + 1, extension=[sqrt(3)])
(1, x**2 - 2*sqrt(3)*x + 4, x**4 - 4*x**2 + 16)
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('sqf_norm', 1, exc)
s, g, r = F.sqf_norm()
if not opt.polys:
return Integer(s), g.as_expr(), r.as_expr()
else:
return Integer(s), g, r
@public
def sqf_part(f, *gens, **args):
"""
Compute square-free part of ``f``.
Examples
========
>>> from sympy import sqf_part
>>> from sympy.abc import x
>>> sqf_part(x**3 - 3*x - 2)
x**2 - x - 2
"""
options.allowed_flags(args, ['polys'])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('sqf_part', 1, exc)
result = F.sqf_part()
if not opt.polys:
return result.as_expr()
else:
return result
def _sorted_factors(factors, method):
"""Sort a list of ``(expr, exp)`` pairs. """
if method == 'sqf':
def key(obj):
poly, exp = obj
rep = poly.rep.rep
return (exp, len(rep), rep)
else:
def key(obj):
poly, exp = obj
rep = poly.rep.rep
return (len(rep), exp, rep)
return sorted(factors, key=key)
def _factors_product(factors):
"""Multiply a list of ``(expr, exp)`` pairs. """
return Mul(*[f.as_expr()**k for f, k in factors])
def _symbolic_factor_list(expr, opt, method):
"""Helper function for :func:`_symbolic_factor`. """
coeff, factors = S.One, []
for arg in Mul.make_args(expr):
if arg.is_Number:
coeff *= arg
continue
elif arg.is_Pow:
base, exp = arg.args
if base.is_Number:
factors.append((base, exp))
continue
else:
base, exp = arg, S.One
try:
poly, _ = _poly_from_expr(base, opt)
except PolificationFailed as exc:
factors.append((exc.expr, exp))
else:
func = getattr(poly, method + '_list')
_coeff, _factors = func()
if _coeff is not S.One:
if exp.is_Integer:
coeff *= _coeff**exp
elif _coeff.is_positive:
factors.append((_coeff, exp))
else:
_factors.append((_coeff, S.One))
if exp is S.One:
factors.extend(_factors)
elif exp.is_integer:
factors.extend([(f, k*exp) for f, k in _factors])
else:
other = []
for f, k in _factors:
if f.as_expr().is_positive:
factors.append((f, k*exp))
else:
other.append((f, k))
factors.append((_factors_product(other), exp))
return coeff, factors
def _symbolic_factor(expr, opt, method):
"""Helper function for :func:`_factor`. """
if isinstance(expr, Expr) and not expr.is_Relational:
if hasattr(expr,'_eval_factor'):
return expr._eval_factor()
coeff, factors = _symbolic_factor_list(together(expr), opt, method)
return _keep_coeff(coeff, _factors_product(factors))
elif hasattr(expr, 'args'):
return expr.func(*[_symbolic_factor(arg, opt, method) for arg in expr.args])
elif hasattr(expr, '__iter__'):
return expr.__class__([_symbolic_factor(arg, opt, method) for arg in expr])
else:
return expr
def _generic_factor_list(expr, gens, args, method):
"""Helper function for :func:`sqf_list` and :func:`factor_list`. """
options.allowed_flags(args, ['frac', 'polys'])
opt = options.build_options(gens, args)
expr = sympify(expr)
if isinstance(expr, Expr) and not expr.is_Relational:
numer, denom = together(expr).as_numer_denom()
cp, fp = _symbolic_factor_list(numer, opt, method)
cq, fq = _symbolic_factor_list(denom, opt, method)
if fq and not opt.frac:
raise PolynomialError("a polynomial expected, got %s" % expr)
_opt = opt.clone(dict(expand=True))
for factors in (fp, fq):
for i, (f, k) in enumerate(factors):
if not f.is_Poly:
f, _ = _poly_from_expr(f, _opt)
factors[i] = (f, k)
fp = _sorted_factors(fp, method)
fq = _sorted_factors(fq, method)
if not opt.polys:
fp = [(f.as_expr(), k) for f, k in fp]
fq = [(f.as_expr(), k) for f, k in fq]
coeff = cp/cq
if not opt.frac:
return coeff, fp
else:
return coeff, fp, fq
else:
raise PolynomialError("a polynomial expected, got %s" % expr)
def _generic_factor(expr, gens, args, method):
"""Helper function for :func:`sqf` and :func:`factor`. """
options.allowed_flags(args, [])
opt = options.build_options(gens, args)
return _symbolic_factor(sympify(expr), opt, method)
def to_rational_coeffs(f):
"""
try to transform a polynomial to have rational coefficients
try to find a transformation ``x = alpha*y``
``f(x) = lc*alpha**n * g(y)`` where ``g`` is a polynomial with
rational coefficients, ``lc`` the leading coefficient.
If this fails, try ``x = y + beta``
``f(x) = g(y)``
Returns ``None`` if ``g`` not found;
``(lc, alpha, None, g)`` in case of rescaling
``(None, None, beta, g)`` in case of translation
Notes
=====
Currently it transforms only polynomials without roots larger than 2.
Examples
========
>>> from sympy import sqrt, Poly, simplify
>>> from sympy.polys.polytools import to_rational_coeffs
>>> from sympy.abc import x
>>> p = Poly(((x**2-1)*(x-2)).subs({x:x*(1 + sqrt(2))}), x, domain='EX')
>>> lc, r, _, g = to_rational_coeffs(p)
>>> lc, r
(7 + 5*sqrt(2), -2*sqrt(2) + 2)
>>> g
Poly(x**3 + x**2 - 1/4*x - 1/4, x, domain='QQ')
>>> r1 = simplify(1/r)
>>> Poly(lc*r**3*(g.as_expr()).subs({x:x*r1}), x, domain='EX') == p
True
"""
from sympy.simplify.simplify import simplify
def _try_rescale(f, f1=None):
"""
try rescaling ``x -> alpha*x`` to convert f to a polynomial
with rational coefficients.
Returns ``alpha, f``; if the rescaling is successful,
``alpha`` is the rescaling factor, and ``f`` is the rescaled
polynomial; else ``alpha`` is ``None``.
"""
from sympy.core.add import Add
if not len(f.gens) == 1 or not (f.gens[0]).is_Atom:
return None, f
n = f.degree()
lc = f.LC()
f1 = f1 or f1.monic()
coeffs = f1.all_coeffs()[1:]
coeffs = [simplify(coeffx) for coeffx in coeffs]
if coeffs[-2]:
rescale1_x = simplify(coeffs[-2]/coeffs[-1])
coeffs1 = []
for i in range(len(coeffs)):
coeffx = simplify(coeffs[i]*rescale1_x**(i + 1))
if not coeffx.is_rational:
break
coeffs1.append(coeffx)
else:
rescale_x = simplify(1/rescale1_x)
x = f.gens[0]
v = [x**n]
for i in range(1, n + 1):
v.append(coeffs1[i - 1]*x**(n - i))
f = Add(*v)
f = Poly(f)
return lc, rescale_x, f
return None
def _try_translate(f, f1=None):
"""
try translating ``x -> x + alpha`` to convert f to a polynomial
with rational coefficients.
Returns ``alpha, f``; if the translating is successful,
``alpha`` is the translating factor, and ``f`` is the shifted
polynomial; else ``alpha`` is ``None``.
"""
from sympy.core.add import Add
if not len(f.gens) == 1 or not (f.gens[0]).is_Atom:
return None, f
n = f.degree()
f1 = f1 or f1.monic()
coeffs = f1.all_coeffs()[1:]
c = simplify(coeffs[0])
if c and not c.is_rational:
func = Add
if c.is_Add:
args = c.args
func = c.func
else:
args = [c]
sifted = sift(args, lambda z: z.is_rational)
c1, c2 = sifted[True], sifted[False]
alpha = -func(*c2)/n
f2 = f1.shift(alpha)
return alpha, f2
return None
def _has_square_roots(p):
"""
Return True if ``f`` is a sum with square roots but no other root
"""
from sympy.core.exprtools import Factors
coeffs = p.coeffs()
has_sq = False
for y in coeffs:
for x in Add.make_args(y):
f = Factors(x).factors
r = [wx.q for b, wx in f.items() if
b.is_number and wx.is_Rational and wx.q >= 2]
if not r:
continue
if min(r) == 2:
has_sq = True
if max(r) > 2:
return False
return has_sq
if f.get_domain().is_EX and _has_square_roots(f):
f1 = f.monic()
r = _try_rescale(f, f1)
if r:
return r[0], r[1], None, r[2]
else:
r = _try_translate(f, f1)
if r:
return None, None, r[0], r[1]
return None
def _torational_factor_list(p, x):
"""
helper function to factor polynomial using to_rational_coeffs
Examples
========
>>> from sympy.polys.polytools import _torational_factor_list
>>> from sympy.abc import x
>>> from sympy import sqrt, expand, Mul
>>> p = expand(((x**2-1)*(x-2)).subs({x:x*(1 + sqrt(2))}))
>>> factors = _torational_factor_list(p, x); factors
(-2, [(-x*(1 + sqrt(2))/2 + 1, 1), (-x*(1 + sqrt(2)) - 1, 1), (-x*(1 + sqrt(2)) + 1, 1)])
>>> expand(factors[0]*Mul(*[z[0] for z in factors[1]])) == p
True
>>> p = expand(((x**2-1)*(x-2)).subs({x:x + sqrt(2)}))
>>> factors = _torational_factor_list(p, x); factors
(1, [(x - 2 + sqrt(2), 1), (x - 1 + sqrt(2), 1), (x + 1 + sqrt(2), 1)])
>>> expand(factors[0]*Mul(*[z[0] for z in factors[1]])) == p
True
"""
from sympy.simplify.simplify import simplify
p1 = Poly(p, x, domain='EX')
n = p1.degree()
res = to_rational_coeffs(p1)
if not res:
return None
lc, r, t, g = res
factors = factor_list(g.as_expr())
if lc:
c = simplify(factors[0]*lc*r**n)
r1 = simplify(1/r)
a = []
for z in factors[1:][0]:
a.append((simplify(z[0].subs({x: x*r1})), z[1]))
else:
c = factors[0]
a = []
for z in factors[1:][0]:
a.append((z[0].subs({x: x - t}), z[1]))
return (c, a)
@public
def sqf_list(f, *gens, **args):
"""
Compute a list of square-free factors of ``f``.
Examples
========
>>> from sympy import sqf_list
>>> from sympy.abc import x
>>> sqf_list(2*x**5 + 16*x**4 + 50*x**3 + 76*x**2 + 56*x + 16)
(2, [(x + 1, 2), (x + 2, 3)])
"""
return _generic_factor_list(f, gens, args, method='sqf')
@public
def sqf(f, *gens, **args):
"""
Compute square-free factorization of ``f``.
Examples
========
>>> from sympy import sqf
>>> from sympy.abc import x
>>> sqf(2*x**5 + 16*x**4 + 50*x**3 + 76*x**2 + 56*x + 16)
2*(x + 1)**2*(x + 2)**3
"""
return _generic_factor(f, gens, args, method='sqf')
@public
def factor_list(f, *gens, **args):
"""
Compute a list of irreducible factors of ``f``.
Examples
========
>>> from sympy import factor_list
>>> from sympy.abc import x, y
>>> factor_list(2*x**5 + 2*x**4*y + 4*x**3 + 4*x**2*y + 2*x + 2*y)
(2, [(x + y, 1), (x**2 + 1, 2)])
"""
return _generic_factor_list(f, gens, args, method='factor')
@public
def factor(f, *gens, **args):
"""
Compute the factorization of expression, ``f``, into irreducibles. (To
factor an integer into primes, use ``factorint``.)
There two modes implemented: symbolic and formal. If ``f`` is not an
instance of :class:`Poly` and generators are not specified, then the
former mode is used. Otherwise, the formal mode is used.
In symbolic mode, :func:`factor` will traverse the expression tree and
factor its components without any prior expansion, unless an instance
of :class:`Add` is encountered (in this case formal factorization is
used). This way :func:`factor` can handle large or symbolic exponents.
By default, the factorization is computed over the rationals. To factor
over other domain, e.g. an algebraic or finite field, use appropriate
options: ``extension``, ``modulus`` or ``domain``.
Examples
========
>>> from sympy import factor, sqrt
>>> from sympy.abc import x, y
>>> factor(2*x**5 + 2*x**4*y + 4*x**3 + 4*x**2*y + 2*x + 2*y)
2*(x + y)*(x**2 + 1)**2
>>> factor(x**2 + 1)
x**2 + 1
>>> factor(x**2 + 1, modulus=2)
(x + 1)**2
>>> factor(x**2 + 1, gaussian=True)
(x - I)*(x + I)
>>> factor(x**2 - 2, extension=sqrt(2))
(x - sqrt(2))*(x + sqrt(2))
>>> factor((x**2 - 1)/(x**2 + 4*x + 4))
(x - 1)*(x + 1)/(x + 2)**2
>>> factor((x**2 + 4*x + 4)**10000000*(x**2 + 1))
(x + 2)**20000000*(x**2 + 1)
By default, factor deals with an expression as a whole:
>>> eq = 2**(x**2 + 2*x + 1)
>>> factor(eq)
2**(x**2 + 2*x + 1)
If the ``deep`` flag is True then subexpressions will
be factored:
>>> factor(eq, deep=True)
2**((x + 1)**2)
See Also
========
sympy.ntheory.factor_.factorint
"""
f = sympify(f)
if args.pop('deep', False):
partials = {}
muladd = f.atoms(Mul, Add)
for p in muladd:
fac = factor(p, *gens, **args)
if (fac.is_Mul or fac.is_Pow) and fac != p:
partials[p] = fac
return f.xreplace(partials)
try:
return _generic_factor(f, gens, args, method='factor')
except PolynomialError as msg:
if not f.is_commutative:
from sympy.core.exprtools import factor_nc
return factor_nc(f)
else:
raise PolynomialError(msg)
@public
def intervals(F, all=False, eps=None, inf=None, sup=None, strict=False, fast=False, sqf=False):
"""
Compute isolating intervals for roots of ``f``.
Examples
========
>>> from sympy import intervals
>>> from sympy.abc import x
>>> intervals(x**2 - 3)
[((-2, -1), 1), ((1, 2), 1)]
>>> intervals(x**2 - 3, eps=1e-2)
[((-26/15, -19/11), 1), ((19/11, 26/15), 1)]
"""
if not hasattr(F, '__iter__'):
try:
F = Poly(F)
except GeneratorsNeeded:
return []
return F.intervals(all=all, eps=eps, inf=inf, sup=sup, fast=fast, sqf=sqf)
else:
polys, opt = parallel_poly_from_expr(F, domain='QQ')
if len(opt.gens) > 1:
raise MultivariatePolynomialError
for i, poly in enumerate(polys):
polys[i] = poly.rep.rep
if eps is not None:
eps = opt.domain.convert(eps)
if eps <= 0:
raise ValueError("'eps' must be a positive rational")
if inf is not None:
inf = opt.domain.convert(inf)
if sup is not None:
sup = opt.domain.convert(sup)
intervals = dup_isolate_real_roots_list(polys, opt.domain,
eps=eps, inf=inf, sup=sup, strict=strict, fast=fast)
result = []
for (s, t), indices in intervals:
s, t = opt.domain.to_sympy(s), opt.domain.to_sympy(t)
result.append(((s, t), indices))
return result
@public
def refine_root(f, s, t, eps=None, steps=None, fast=False, check_sqf=False):
"""
Refine an isolating interval of a root to the given precision.
Examples
========
>>> from sympy import refine_root
>>> from sympy.abc import x
>>> refine_root(x**2 - 3, 1, 2, eps=1e-2)
(19/11, 26/15)
"""
try:
F = Poly(f)
except GeneratorsNeeded:
raise PolynomialError(
"can't refine a root of %s, not a polynomial" % f)
return F.refine_root(s, t, eps=eps, steps=steps, fast=fast, check_sqf=check_sqf)
@public
def count_roots(f, inf=None, sup=None):
"""
Return the number of roots of ``f`` in ``[inf, sup]`` interval.
If one of ``inf`` or ``sup`` is complex, it will return the number of roots
in the complex rectangle with corners at ``inf`` and ``sup``.
Examples
========
>>> from sympy import count_roots, I
>>> from sympy.abc import x
>>> count_roots(x**4 - 4, -3, 3)
2
>>> count_roots(x**4 - 4, 0, 1 + 3*I)
1
"""
try:
F = Poly(f, greedy=False)
except GeneratorsNeeded:
raise PolynomialError("can't count roots of %s, not a polynomial" % f)
return F.count_roots(inf=inf, sup=sup)
@public
def real_roots(f, multiple=True):
"""
Return a list of real roots with multiplicities of ``f``.
Examples
========
>>> from sympy import real_roots
>>> from sympy.abc import x
>>> real_roots(2*x**3 - 7*x**2 + 4*x + 4)
[-1/2, 2, 2]
"""
try:
F = Poly(f, greedy=False)
except GeneratorsNeeded:
raise PolynomialError(
"can't compute real roots of %s, not a polynomial" % f)
return F.real_roots(multiple=multiple)
@public
def nroots(f, n=15, maxsteps=50, cleanup=True):
"""
Compute numerical approximations of roots of ``f``.
Examples
========
>>> from sympy import nroots
>>> from sympy.abc import x
>>> nroots(x**2 - 3, n=15)
[-1.73205080756888, 1.73205080756888]
>>> nroots(x**2 - 3, n=30)
[-1.73205080756887729352744634151, 1.73205080756887729352744634151]
"""
try:
F = Poly(f, greedy=False)
except GeneratorsNeeded:
raise PolynomialError(
"can't compute numerical roots of %s, not a polynomial" % f)
return F.nroots(n=n, maxsteps=maxsteps, cleanup=cleanup)
@public
def ground_roots(f, *gens, **args):
"""
Compute roots of ``f`` by factorization in the ground domain.
Examples
========
>>> from sympy import ground_roots
>>> from sympy.abc import x
>>> ground_roots(x**6 - 4*x**4 + 4*x**3 - x**2)
{0: 2, 1: 2}
"""
options.allowed_flags(args, [])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('ground_roots', 1, exc)
return F.ground_roots()
@public
def nth_power_roots_poly(f, n, *gens, **args):
"""
Construct a polynomial with n-th powers of roots of ``f``.
Examples
========
>>> from sympy import nth_power_roots_poly, factor, roots
>>> from sympy.abc import x
>>> f = x**4 - x**2 + 1
>>> g = factor(nth_power_roots_poly(f, 2))
>>> g
(x**2 - x + 1)**2
>>> R_f = [ (r**2).expand() for r in roots(f) ]
>>> R_g = roots(g).keys()
>>> set(R_f) == set(R_g)
True
"""
options.allowed_flags(args, [])
try:
F, opt = poly_from_expr(f, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('nth_power_roots_poly', 1, exc)
result = F.nth_power_roots_poly(n)
if not opt.polys:
return result.as_expr()
else:
return result
@public
def cancel(f, *gens, **args):
"""
Cancel common factors in a rational function ``f``.
Examples
========
>>> from sympy import cancel, sqrt, Symbol
>>> from sympy.abc import x
>>> A = Symbol('A', commutative=False)
>>> cancel((2*x**2 - 2)/(x**2 - 2*x + 1))
(2*x + 2)/(x - 1)
>>> cancel((sqrt(3) + sqrt(15)*A)/(sqrt(2) + sqrt(10)*A))
sqrt(6)/2
"""
from sympy.core.exprtools import factor_terms
from sympy.functions.elementary.piecewise import Piecewise
options.allowed_flags(args, ['polys'])
f = sympify(f)
if not isinstance(f, (tuple, Tuple)):
if f.is_Number or isinstance(f, Relational) or not isinstance(f, Expr):
return f
f = factor_terms(f, radical=True)
p, q = f.as_numer_denom()
elif len(f) == 2:
p, q = f
elif isinstance(f, Tuple):
return factor_terms(f)
else:
raise ValueError('unexpected argument: %s' % f)
try:
(F, G), opt = parallel_poly_from_expr((p, q), *gens, **args)
except PolificationFailed:
if not isinstance(f, (tuple, Tuple)):
return f
else:
return S.One, p, q
except PolynomialError as msg:
if f.is_commutative and not f.has(Piecewise):
raise PolynomialError(msg)
# Handling of noncommutative and/or piecewise expressions
if f.is_Add or f.is_Mul:
sifted = sift(f.args, lambda x: x.is_commutative is True and not x.has(Piecewise))
c, nc = sifted[True], sifted[False]
nc = [cancel(i) for i in nc]
return f.func(cancel(f.func._from_args(c)), *nc)
else:
reps = []
pot = preorder_traversal(f)
next(pot)
for e in pot:
# XXX: This should really skip anything that's not Expr.
if isinstance(e, (tuple, Tuple, BooleanAtom)):
continue
try:
reps.append((e, cancel(e)))
pot.skip() # this was handled successfully
except NotImplementedError:
pass
return f.xreplace(dict(reps))
c, P, Q = F.cancel(G)
if not isinstance(f, (tuple, Tuple)):
return c*(P.as_expr()/Q.as_expr())
else:
if not opt.polys:
return c, P.as_expr(), Q.as_expr()
else:
return c, P, Q
@public
def reduced(f, G, *gens, **args):
"""
Reduces a polynomial ``f`` modulo a set of polynomials ``G``.
Given a polynomial ``f`` and a set of polynomials ``G = (g_1, ..., g_n)``,
computes a set of quotients ``q = (q_1, ..., q_n)`` and the remainder ``r``
such that ``f = q_1*g_1 + ... + q_n*g_n + r``, where ``r`` vanishes or ``r``
is a completely reduced polynomial with respect to ``G``.
Examples
========
>>> from sympy import reduced
>>> from sympy.abc import x, y
>>> reduced(2*x**4 + y**2 - x**2 + y**3, [x**3 - x, y**3 - y])
([2*x, 1], x**2 + y**2 + y)
"""
options.allowed_flags(args, ['polys', 'auto'])
try:
polys, opt = parallel_poly_from_expr([f] + list(G), *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('reduced', 0, exc)
domain = opt.domain
retract = False
if opt.auto and domain.has_Ring and not domain.has_Field:
opt = opt.clone(dict(domain=domain.get_field()))
retract = True
from sympy.polys.rings import xring
_ring, _ = xring(opt.gens, opt.domain, opt.order)
for i, poly in enumerate(polys):
poly = poly.set_domain(opt.domain).rep.to_dict()
polys[i] = _ring.from_dict(poly)
Q, r = polys[0].div(polys[1:])
Q = [Poly._from_dict(dict(q), opt) for q in Q]
r = Poly._from_dict(dict(r), opt)
if retract:
try:
_Q, _r = [q.to_ring() for q in Q], r.to_ring()
except CoercionFailed:
pass
else:
Q, r = _Q, _r
if not opt.polys:
return [q.as_expr() for q in Q], r.as_expr()
else:
return Q, r
@public
def groebner(F, *gens, **args):
"""
Computes the reduced Groebner basis for a set of polynomials.
Use the ``order`` argument to set the monomial ordering that will be
used to compute the basis. Allowed orders are ``lex``, ``grlex`` and
``grevlex``. If no order is specified, it defaults to ``lex``.
For more information on Groebner bases, see the references and the docstring
of `solve_poly_system()`.
Examples
========
Example taken from [1].
>>> from sympy import groebner
>>> from sympy.abc import x, y
>>> F = [x*y - 2*y, 2*y**2 - x**2]
>>> groebner(F, x, y, order='lex')
GroebnerBasis([x**2 - 2*y**2, x*y - 2*y, y**3 - 2*y], x, y,
domain='ZZ', order='lex')
>>> groebner(F, x, y, order='grlex')
GroebnerBasis([y**3 - 2*y, x**2 - 2*y**2, x*y - 2*y], x, y,
domain='ZZ', order='grlex')
>>> groebner(F, x, y, order='grevlex')
GroebnerBasis([y**3 - 2*y, x**2 - 2*y**2, x*y - 2*y], x, y,
domain='ZZ', order='grevlex')
By default, an improved implementation of the Buchberger algorithm is
used. Optionally, an implementation of the F5B algorithm can be used.
The algorithm can be set using ``method`` flag or with the :func:`setup`
function from :mod:`sympy.polys.polyconfig`:
>>> F = [x**2 - x - 1, (2*x - 1) * y - (x**10 - (1 - x)**10)]
>>> groebner(F, x, y, method='buchberger')
GroebnerBasis([x**2 - x - 1, y - 55], x, y, domain='ZZ', order='lex')
>>> groebner(F, x, y, method='f5b')
GroebnerBasis([x**2 - x - 1, y - 55], x, y, domain='ZZ', order='lex')
References
==========
1. [Buchberger01]_
2. [Cox97]_
"""
return GroebnerBasis(F, *gens, **args)
@public
def is_zero_dimensional(F, *gens, **args):
"""
Checks if the ideal generated by a Groebner basis is zero-dimensional.
The algorithm checks if the set of monomials not divisible by the
leading monomial of any element of ``F`` is bounded.
References
==========
David A. Cox, John B. Little, Donal O'Shea. Ideals, Varieties and
Algorithms, 3rd edition, p. 230
"""
return GroebnerBasis(F, *gens, **args).is_zero_dimensional
@public
class GroebnerBasis(Basic):
"""Represents a reduced Groebner basis. """
def __new__(cls, F, *gens, **args):
"""Compute a reduced Groebner basis for a system of polynomials. """
options.allowed_flags(args, ['polys', 'method'])
try:
polys, opt = parallel_poly_from_expr(F, *gens, **args)
except PolificationFailed as exc:
raise ComputationFailed('groebner', len(F), exc)
from sympy.polys.rings import PolyRing
ring = PolyRing(opt.gens, opt.domain, opt.order)
for i, poly in enumerate(polys):
polys[i] = ring.from_dict(poly.rep.to_dict())
G = _groebner(polys, ring, method=opt.method)
G = [Poly._from_dict(g, opt) for g in G]
return cls._new(G, opt)
@classmethod
def _new(cls, basis, options):
obj = Basic.__new__(cls)
obj._basis = tuple(basis)
obj._options = options
return obj
@property
def args(self):
return (Tuple(*self._basis), Tuple(*self._options.gens))
@property
def exprs(self):
return [poly.as_expr() for poly in self._basis]
@property
def polys(self):
return list(self._basis)
@property
def gens(self):
return self._options.gens
@property
def domain(self):
return self._options.domain
@property
def order(self):
return self._options.order
def __len__(self):
return len(self._basis)
def __iter__(self):
if self._options.polys:
return iter(self.polys)
else:
return iter(self.exprs)
def __getitem__(self, item):
if self._options.polys:
basis = self.polys
else:
basis = self.exprs
return basis[item]
def __hash__(self):
return hash((self._basis, tuple(self._options.items())))
def __eq__(self, other):
if isinstance(other, self.__class__):
return self._basis == other._basis and self._options == other._options
elif iterable(other):
return self.polys == list(other) or self.exprs == list(other)
else:
return False
def __ne__(self, other):
return not self.__eq__(other)
@property
def is_zero_dimensional(self):
"""
Checks if the ideal generated by a Groebner basis is zero-dimensional.
The algorithm checks if the set of monomials not divisible by the
leading monomial of any element of ``F`` is bounded.
References
==========
David A. Cox, John B. Little, Donal O'Shea. Ideals, Varieties and
Algorithms, 3rd edition, p. 230
"""
def single_var(monomial):
return sum(map(bool, monomial)) == 1
exponents = Monomial([0]*len(self.gens))
order = self._options.order
for poly in self.polys:
monomial = poly.LM(order=order)
if single_var(monomial):
exponents *= monomial
# If any element of the exponents vector is zero, then there's
# a variable for which there's no degree bound and the ideal
# generated by this Groebner basis isn't zero-dimensional.
return all(exponents)
def fglm(self, order):
"""
Convert a Groebner basis from one ordering to another.
The FGLM algorithm converts reduced Groebner bases of zero-dimensional
ideals from one ordering to another. This method is often used when it
is infeasible to compute a Groebner basis with respect to a particular
ordering directly.
Examples
========
>>> from sympy.abc import x, y
>>> from sympy import groebner
>>> F = [x**2 - 3*y - x + 1, y**2 - 2*x + y - 1]
>>> G = groebner(F, x, y, order='grlex')
>>> list(G.fglm('lex'))
[2*x - y**2 - y + 1, y**4 + 2*y**3 - 3*y**2 - 16*y + 7]
>>> list(groebner(F, x, y, order='lex'))
[2*x - y**2 - y + 1, y**4 + 2*y**3 - 3*y**2 - 16*y + 7]
References
==========
J.C. Faugere, P. Gianni, D. Lazard, T. Mora (1994). Efficient
Computation of Zero-dimensional Groebner Bases by Change of
Ordering
"""
opt = self._options
src_order = opt.order
dst_order = monomial_key(order)
if src_order == dst_order:
return self
if not self.is_zero_dimensional:
raise NotImplementedError("can't convert Groebner bases of ideals with positive dimension")
polys = list(self._basis)
domain = opt.domain
opt = opt.clone(dict(
domain=domain.get_field(),
order=dst_order,
))
from sympy.polys.rings import xring
_ring, _ = xring(opt.gens, opt.domain, src_order)
for i, poly in enumerate(polys):
poly = poly.set_domain(opt.domain).rep.to_dict()
polys[i] = _ring.from_dict(poly)
G = matrix_fglm(polys, _ring, dst_order)
G = [Poly._from_dict(dict(g), opt) for g in G]
if not domain.has_Field:
G = [g.clear_denoms(convert=True)[1] for g in G]
opt.domain = domain
return self._new(G, opt)
def reduce(self, expr, auto=True):
"""
Reduces a polynomial modulo a Groebner basis.
Given a polynomial ``f`` and a set of polynomials ``G = (g_1, ..., g_n)``,
computes a set of quotients ``q = (q_1, ..., q_n)`` and the remainder ``r``
such that ``f = q_1*f_1 + ... + q_n*f_n + r``, where ``r`` vanishes or ``r``
is a completely reduced polynomial with respect to ``G``.
Examples
========
>>> from sympy import groebner, expand
>>> from sympy.abc import x, y
>>> f = 2*x**4 - x**2 + y**3 + y**2
>>> G = groebner([x**3 - x, y**3 - y])
>>> G.reduce(f)
([2*x, 1], x**2 + y**2 + y)
>>> Q, r = _
>>> expand(sum(q*g for q, g in zip(Q, G)) + r)
2*x**4 - x**2 + y**3 + y**2
>>> _ == f
True
"""
poly = Poly._from_expr(expr, self._options)
polys = [poly] + list(self._basis)
opt = self._options
domain = opt.domain
retract = False
if auto and domain.has_Ring and not domain.has_Field:
opt = opt.clone(dict(domain=domain.get_field()))
retract = True
from sympy.polys.rings import xring
_ring, _ = xring(opt.gens, opt.domain, opt.order)
for i, poly in enumerate(polys):
poly = poly.set_domain(opt.domain).rep.to_dict()
polys[i] = _ring.from_dict(poly)
Q, r = polys[0].div(polys[1:])
Q = [Poly._from_dict(dict(q), opt) for q in Q]
r = Poly._from_dict(dict(r), opt)
if retract:
try:
_Q, _r = [q.to_ring() for q in Q], r.to_ring()
except CoercionFailed:
pass
else:
Q, r = _Q, _r
if not opt.polys:
return [q.as_expr() for q in Q], r.as_expr()
else:
return Q, r
def contains(self, poly):
"""
Check if ``poly`` belongs the ideal generated by ``self``.
Examples
========
>>> from sympy import groebner
>>> from sympy.abc import x, y
>>> f = 2*x**3 + y**3 + 3*y
>>> G = groebner([x**2 + y**2 - 1, x*y - 2])
>>> G.contains(f)
True
>>> G.contains(f + 1)
False
"""
return self.reduce(poly)[1] == 0
@public
def poly(expr, *gens, **args):
"""
Efficiently transform an expression into a polynomial.
Examples
========
>>> from sympy import poly
>>> from sympy.abc import x
>>> poly(x*(x**2 + x - 1)**2)
Poly(x**5 + 2*x**4 - x**3 - 2*x**2 + x, x, domain='ZZ')
"""
options.allowed_flags(args, [])
def _poly(expr, opt):
terms, poly_terms = [], []
for term in Add.make_args(expr):
factors, poly_factors = [], []
for factor in Mul.make_args(term):
if factor.is_Add:
poly_factors.append(_poly(factor, opt))
elif factor.is_Pow and factor.base.is_Add and factor.exp.is_Integer:
poly_factors.append(
_poly(factor.base, opt).pow(factor.exp))
else:
factors.append(factor)
if not poly_factors:
terms.append(term)
else:
product = poly_factors[0]
for factor in poly_factors[1:]:
product = product.mul(factor)
if factors:
factor = Mul(*factors)
if factor.is_Number:
product = product.mul(factor)
else:
product = product.mul(Poly._from_expr(factor, opt))
poly_terms.append(product)
if not poly_terms:
result = Poly._from_expr(expr, opt)
else:
result = poly_terms[0]
for term in poly_terms[1:]:
result = result.add(term)
if terms:
term = Add(*terms)
if term.is_Number:
result = result.add(term)
else:
result = result.add(Poly._from_expr(term, opt))
return result.reorder(*opt.get('gens', ()), **args)
expr = sympify(expr)
if expr.is_Poly:
return Poly(expr, *gens, **args)
if 'expand' not in args:
args['expand'] = False
opt = options.build_options(gens, args)
return _poly(expr, opt)
|
sahilshekhawat/sympy
|
sympy/polys/polytools.py
|
Python
|
bsd-3-clause
| 172,191
|
[
"Gaussian"
] |
e77e2f9ab8e6d1004f6873edd977c71cf6e7b55024804c3cea302bffc501612c
|
# This file is part of Androguard.
#
# Copyright (C) 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS-IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
'''This file is a simplified version of writer.py that outputs an AST instead of source code.'''
import struct
from tools.modified.androguard.decompiler.dad import basic_blocks, instruction, opcode_ins
def array_access(arr, ind): return ['ArrayAccess', [arr, ind]]
def array_creation(tn, params, dim): return ['ArrayCreation', [tn] + params, dim]
def array_initializer(params, tn=None): return ['ArrayInitializer', params, tn]
def assignment(lhs, rhs, op=''): return ['Assignment', [lhs, rhs], op]
def binary_infix(op, left, right): return ['BinaryInfix', [left, right], op]
def cast(tn, arg): return ['Cast', [tn, arg]]
def field_access(triple, left): return ['FieldAccess', [left], triple]
def literal(result, tt): return ['Literal', result, tt]
def local(name): return ['Local', name]
def method_invocation(triple, name, base, params):
if base is None:
return ['MethodInvocation', params, triple, name, False]
return ['MethodInvocation', [base]+params, triple, name, True]
def parenthesis(expr): return ['Parenthesis', [expr]]
def typen(baset, dim): return ['TypeName', (baset, dim)]
def unary_prefix(op, left): return ['Unary', [left], op, False]
def unary_postfix(left, op): return ['Unary', [left], op, True]
def var_decl(typen, var): return [typen, var]
def dummy(*args): return ['Dummy', args]
################################################################################
def expression_stmt(expr): return ['ExpressionStatement', expr]
def local_decl_stmt(expr, decl): return ['LocalDeclarationStatement', expr, decl]
def return_stmt(expr): return ['ReturnStatement', expr]
def throw_stmt(expr): return ['ThrowStatement', expr]
def jump_stmt(keyword): return ['JumpStatement', keyword, None]
def loop_stmt(isdo, cond_expr, body):
type_ = 'DoStatement' if isdo else 'WhileStatement'
return [type_, None, cond_expr, body]
def try_stmt(tryb, pairs): return ['TryStatement', None, tryb, pairs]
def if_stmt(cond_expr, scopes): return ['IfStatement', None, cond_expr, scopes]
def switch_stmt(cond_expr, ksv_pairs):
return ['SwitchStatement', None, cond_expr, ksv_pairs]
# Create empty statement block (statements to be appended later)
# Note, the code below assumes this can be modified in place
def statement_block(): return ['BlockStatement', None, []]
# Add a statement to the end of a statement block
def _append(sb, stmt):
assert(sb[0] == 'BlockStatement')
if stmt is not None:
sb[2].append(stmt)
################################################################################
TYPE_DESCRIPTOR = {
'V': 'void',
'Z': 'boolean',
'B': 'byte',
'S': 'short',
'C': 'char',
'I': 'int',
'J': 'long',
'F': 'float',
'D': 'double',
}
def parse_descriptor(desc):
dim = 0
while desc and desc[0] == '[':
desc = desc[1:]
dim += 1
if desc in TYPE_DESCRIPTOR:
return typen('.'+TYPE_DESCRIPTOR[desc], dim)
if desc and desc[0] == 'L' and desc[-1] == ';':
return typen(desc[1:-1], dim)
# invalid descriptor (probably None)
return dummy(str(desc))
# Note: the literal_foo functions (and dummy) are also imported by decompile.py
def literal_string(s):
escapes = {
'\0':'\\0',
'\t':'\\t',
'\r':'\\r',
'\n':'\\n',
'"':'\\"',
'\\':'\\\\'
}
buf = ['"']
for c in s.decode('utf8'):
if c in escapes:
buf.append(escapes[c])
elif ' ' <= c < '\x7f':
buf.append(c)
else:
buf.append('\u{:04x}'.format(ord(c)))
buf.append('"')
return literal(''.join(buf), ('java/lang/String', 0))
def literal_class(desc):
return literal(parse_descriptor(desc), ('java/lang/Class', 0))
def literal_bool(b): return literal(str(b).lower(), ('.boolean', 0))
def literal_int(b): return literal(str(b), ('.int', 0))
def literal_hex_int(b): return literal(hex(b), ('.int', 0))
def literal_long(b): return literal(str(b)+'L', ('.long', 0))
def literal_float(f): return literal(str(f)+'f', ('.float', 0))
def literal_double(f): return literal(str(f), ('.double', 0))
def literal_null(): return literal('null', ('.null', 0))
def visit_decl(var, init_expr=None):
t = parse_descriptor(var.get_type())
v = local('v{}'.format(var.name))
return local_decl_stmt(init_expr, var_decl(t, v))
def visit_arr_data(value):
data = value.get_data()
tab = []
elem_size = value.element_width
if elem_size == 4:
for i in range(0, value.size * 4, 4):
tab.append(struct.unpack('<i', data[i:i + 4])[0])
else: # FIXME: other cases
for i in range(value.size):
tab.append(struct.unpack('<b', data[i])[0])
return array_initializer(map(literal_int, tab))
def write_inplace_if_possible(lhs, rhs):
if isinstance(rhs, instruction.BinaryExpression) and lhs == rhs.var_map[rhs.arg1]:
exp_rhs = rhs.var_map[rhs.arg2]
# post increment/decrement
if rhs.op in '+-' and isinstance(exp_rhs, instruction.Constant) and exp_rhs.get_int_value() == 1:
return unary_postfix(visit_expr(lhs), rhs.op * 2)
# compound assignment
return assignment(visit_expr(lhs), visit_expr(exp_rhs), op=rhs.op)
return assignment(visit_expr(lhs), visit_expr(rhs))
def visit_expr(op):
if isinstance(op, instruction.ArrayLengthExpression):
expr = visit_expr(op.var_map[op.array])
return field_access([None, 'length', None], expr)
if isinstance(op, instruction.ArrayLoadExpression):
array_expr = visit_expr(op.var_map[op.array])
index_expr = visit_expr(op.var_map[op.idx])
return array_access(array_expr, index_expr)
if isinstance(op, instruction.ArrayStoreInstruction):
array_expr = visit_expr(op.var_map[op.array])
index_expr = visit_expr(op.var_map[op.index])
rhs = visit_expr(op.var_map[op.rhs])
return assignment(array_access(array_expr, index_expr), rhs)
if isinstance(op, instruction.AssignExpression):
lhs = op.var_map.get(op.lhs)
rhs = op.rhs
if lhs is None:
return visit_expr(rhs)
return write_inplace_if_possible(lhs, rhs)
if isinstance(op, instruction.BaseClass):
if op.clsdesc is None:
assert(op.cls == "super")
return local(op.cls)
return parse_descriptor(op.clsdesc)
if isinstance(op, instruction.BinaryExpression):
lhs = op.var_map.get(op.arg1)
rhs = op.var_map.get(op.arg2)
expr = binary_infix(op.op, visit_expr(lhs), visit_expr(rhs))
if not isinstance(op, instruction.BinaryCompExpression):
expr = parenthesis(expr)
return expr
if isinstance(op, instruction.CheckCastExpression):
lhs = op.var_map.get(op.arg)
return parenthesis(cast(parse_descriptor(op.clsdesc), visit_expr(lhs)))
if isinstance(op, instruction.ConditionalExpression):
lhs = op.var_map.get(op.arg1)
rhs = op.var_map.get(op.arg2)
return binary_infix(op.op, visit_expr(lhs), visit_expr(rhs))
if isinstance(op, instruction.ConditionalZExpression):
arg = op.var_map[op.arg]
if isinstance(arg, instruction.BinaryCompExpression):
arg.op = op.op
return visit_expr(arg)
expr = visit_expr(arg)
atype = arg.get_type()
if atype == 'Z':
if op.op == opcode_ins.Op.EQUAL:
expr = unary_prefix('!', expr)
elif atype in 'VBSCIJFD':
expr = binary_infix(op.op, expr, literal_int(0))
else:
expr = binary_infix(op.op, expr, literal_null())
return expr
if isinstance(op, instruction.Constant):
if op.type == 'Ljava/lang/String;':
return literal_string(op.cst)
elif op.type == 'Z':
return literal_bool(op.cst == 0)
elif op.type in 'ISCB':
return literal_int(op.cst2)
elif op.type in 'J':
return literal_long(op.cst2)
elif op.type in 'F':
return literal_float(op.cst)
elif op.type in 'D':
return literal_double(op.cst)
elif op.type == 'Ljava/lang/Class;':
return literal_class(op.clsdesc)
return dummy('???')
if isinstance(op, instruction.FillArrayExpression):
array_expr = visit_expr(op.var_map[op.reg])
rhs = visit_arr_data(op.value)
return assignment(array_expr, rhs)
if isinstance(op, instruction.FilledArrayExpression):
tn = parse_descriptor(op.type)
params = [visit_expr(op.var_map[x]) for x in op.args]
return array_initializer(params, tn)
if isinstance(op, instruction.InstanceExpression):
triple = op.clsdesc[1:-1], op.name, op.ftype
expr = visit_expr(op.var_map[op.arg])
return field_access(triple, expr)
if isinstance(op, instruction.InstanceInstruction):
triple = op.clsdesc[1:-1], op.name, op.atype
lhs = field_access(triple, visit_expr(op.var_map[op.lhs]))
rhs = visit_expr(op.var_map[op.rhs])
return assignment(lhs, rhs)
if isinstance(op, instruction.InvokeInstruction):
base = op.var_map[op.base]
params = [op.var_map[arg] for arg in op.args]
params = map(visit_expr, params)
if op.name == '<init>':
if isinstance(base, instruction.ThisParam):
return method_invocation(op.triple, 'this', None, params)
elif isinstance(base, instruction.NewInstance):
return ['ClassInstanceCreation', params, parse_descriptor(base.type)]
else:
assert(isinstance(base, instruction.Variable))
# fallthrough to create dummy <init> call
return method_invocation(op.triple, op.name, visit_expr(base), params)
# for unmatched monitor instructions, just create dummy expressions
if isinstance(op, instruction.MonitorEnterExpression):
return dummy("monitor enter(", visit_expr(op.var_map[op.ref]), ")")
if isinstance(op, instruction.MonitorExitExpression):
return dummy("monitor exit(", visit_expr(op.var_map[op.ref]), ")")
if isinstance(op, instruction.MoveExpression):
lhs = op.var_map.get(op.lhs)
rhs = op.var_map.get(op.rhs)
return write_inplace_if_possible(lhs, rhs)
if isinstance(op, instruction.MoveResultExpression):
lhs = op.var_map.get(op.lhs)
rhs = op.var_map.get(op.rhs)
return assignment(visit_expr(lhs), visit_expr(rhs))
if isinstance(op, instruction.NewArrayExpression):
tn = parse_descriptor(op.type[1:])
expr = visit_expr(op.var_map[op.size])
return array_creation(tn, [expr], 1)
# create dummy expression for unmatched newinstance
if isinstance(op, instruction.NewInstance):
return dummy("new ", parse_descriptor(op.type))
if isinstance(op, instruction.Param):
if isinstance(op, instruction.ThisParam):
return local('this')
return local('p{}'.format(op.v))
if isinstance(op, instruction.StaticExpression):
triple = op.clsdesc[1:-1], op.name, op.ftype
return field_access(triple, parse_descriptor(op.clsdesc))
if isinstance(op, instruction.StaticInstruction):
triple = op.clsdesc[1:-1], op.name, op.ftype
lhs = field_access(triple, parse_descriptor(op.clsdesc))
rhs = visit_expr(op.var_map[op.rhs])
return assignment(lhs, rhs)
if isinstance(op, instruction.SwitchExpression):
return visit_expr(op.var_map[op.src])
if isinstance(op, instruction.UnaryExpression):
lhs = op.var_map.get(op.arg)
if isinstance(op, instruction.CastExpression):
expr = cast(parse_descriptor(op.clsdesc), visit_expr(lhs))
else:
expr = unary_prefix(op.op, visit_expr(lhs))
return parenthesis(expr)
if isinstance(op, instruction.Variable):
# assert(op.declared)
return local('v{}'.format(op.name))
return dummy('???')
def visit_ins(op, isCtor=False):
if isinstance(op, instruction.ReturnInstruction):
expr = None if op.arg is None else visit_expr(op.var_map[op.arg])
return return_stmt(expr)
elif isinstance(op, instruction.ThrowExpression):
return throw_stmt(visit_expr(op.var_map[op.ref]))
elif isinstance(op, instruction.NopExpression):
return None
# Local var decl statements
if isinstance(op, (instruction.AssignExpression, instruction.MoveExpression, instruction.MoveResultExpression)):
lhs = op.var_map.get(op.lhs)
rhs = op.rhs if isinstance(op, instruction.AssignExpression) else op.var_map.get(op.rhs)
if isinstance(lhs, instruction.Variable) and not lhs.declared:
lhs.declared = True
expr = visit_expr(rhs)
return visit_decl(lhs, expr)
# skip this() at top of constructors
if isCtor and isinstance(op, instruction.AssignExpression):
op2 = op.rhs
if op.lhs is None and isinstance(op2, instruction.InvokeInstruction):
if op2.name == '<init>' and len(op2.args) == 0:
if isinstance(op2.var_map[op2.base], instruction.ThisParam):
return None
# MoveExpression is skipped when lhs = rhs
if isinstance(op, instruction.MoveExpression):
if op.var_map.get(op.lhs) is op.var_map.get(op.rhs):
return None
return expression_stmt(visit_expr(op))
class JSONWriter(object):
def __init__(self, graph, method):
self.graph = graph
self.method = method
self.visited_nodes = set()
self.loop_follow = [None]
self.if_follow = [None]
self.switch_follow = [None]
self.latch_node = [None]
self.try_follow = [None]
self.next_case = None
self.need_break = True
self.constructor = False
self.context = []
# This class is created as a context manager so that it can be used like
# with self as foo:
# ...
# which pushes a statement block on to the context stack and assigns it to foo
# within the with block, all added instructions will be added to foo
def __enter__(self):
self.context.append(statement_block())
return self.context[-1]
def __exit__(self, *args):
self.context.pop()
return False
# Add a statement to the current context
def add(self, val): _append(self.context[-1], val)
def visit_ins(self, op):
self.add(visit_ins(op, isCtor=self.constructor))
# Note: this is a mutating operation
def get_ast(self):
m = self.method
flags = m.access
if 'constructor' in flags:
flags.remove('constructor')
self.constructor = True
params = m.lparams[:]
if 'static' not in m.access:
params = params[1:]
# DAD doesn't create any params for abstract methods
if len(params) != len(m.params_type):
assert('abstract' in flags or 'native' in flags)
assert(not params)
params = range(len(m.params_type))
paramdecls = []
for ptype, name in zip(m.params_type, params):
t = parse_descriptor(ptype)
v = local('p{}'.format(name))
paramdecls.append(var_decl(t, v))
if self.graph is None:
body = None
else:
with self as body:
self.visit_node(self.graph.entry)
return {
'triple': m.triple,
'flags': flags,
'ret': parse_descriptor(m.type),
'params': paramdecls,
'comments': [],
'body': body,
}
def _visit_condition(self, cond):
if cond.isnot:
cond.cond1.neg()
left = parenthesis(self.get_cond(cond.cond1))
right = parenthesis(self.get_cond(cond.cond2))
op = '&&' if cond.isand else '||'
res = binary_infix(op, left, right)
return res
def get_cond(self, node):
if isinstance(node, basic_blocks.ShortCircuitBlock):
return self._visit_condition(node.cond)
elif isinstance(node, basic_blocks.LoopBlock):
return self.get_cond(node.cond)
else:
assert(type(node) == basic_blocks.CondBlock)
assert(len(node.ins) == 1)
return visit_expr(node.ins[-1])
def visit_node(self, node):
if node in (self.if_follow[-1], self.switch_follow[-1],
self.loop_follow[-1], self.latch_node[-1],
self.try_follow[-1]):
return
if not node.type.is_return and node in self.visited_nodes:
return
self.visited_nodes.add(node)
for var in node.var_to_declare:
if not var.declared:
self.add(visit_decl(var))
var.declared = True
node.visit(self)
def visit_loop_node(self, loop):
isDo = cond_expr = body = None
follow = loop.follow['loop']
if loop.looptype.is_pretest:
if loop.true is follow:
loop.neg()
loop.true, loop.false = loop.false, loop.true
isDo = False
cond_expr = self.get_cond(loop)
elif loop.looptype.is_posttest:
isDo = True
self.latch_node.append(loop.latch)
elif loop.looptype.is_endless:
isDo = False
cond_expr = literal_bool(True)
with self as body:
self.loop_follow.append(follow)
if loop.looptype.is_pretest:
self.visit_node(loop.true)
else:
self.visit_node(loop.cond)
self.loop_follow.pop()
if loop.looptype.is_pretest:
pass
elif loop.looptype.is_posttest:
self.latch_node.pop()
cond_expr = self.get_cond(loop.latch)
else:
self.visit_node(loop.latch)
assert(cond_expr is not None and isDo is not None)
self.add(loop_stmt(isDo, cond_expr, body))
if follow is not None:
self.visit_node(follow)
def visit_cond_node(self, cond):
cond_expr = None
scopes = []
follow = cond.follow['if']
if cond.false is cond.true:
self.add(expression_stmt(self.get_cond(cond)))
self.visit_node(cond.true)
return
if cond.false is self.loop_follow[-1]:
cond.neg()
cond.true, cond.false = cond.false, cond.true
if self.loop_follow[-1] in (cond.true, cond.false):
cond_expr = self.get_cond(cond)
with self as scope:
self.add(jump_stmt('break'))
scopes.append(scope)
with self as scope:
self.visit_node(cond.false)
scopes.append(scope)
self.add(if_stmt(cond_expr, scopes))
elif follow is not None:
if cond.true in (follow, self.next_case) or\
cond.num > cond.true.num:
# or cond.true.num > cond.false.num:
cond.neg()
cond.true, cond.false = cond.false, cond.true
self.if_follow.append(follow)
if cond.true: # in self.visited_nodes:
cond_expr = self.get_cond(cond)
with self as scope:
self.visit_node(cond.true)
scopes.append(scope)
is_else = not (follow in (cond.true, cond.false))
if is_else and not cond.false in self.visited_nodes:
with self as scope:
self.visit_node(cond.false)
scopes.append(scope)
self.if_follow.pop()
self.add(if_stmt(cond_expr, scopes))
self.visit_node(follow)
else:
cond_expr = self.get_cond(cond)
with self as scope:
self.visit_node(cond.true)
scopes.append(scope)
with self as scope:
self.visit_node(cond.false)
scopes.append(scope)
self.add(if_stmt(cond_expr, scopes))
def visit_switch_node(self, switch):
lins = switch.get_ins()
for ins in lins[:-1]:
self.visit_ins(ins)
switch_ins = switch.get_ins()[-1]
cond_expr = visit_expr(switch_ins)
ksv_pairs = []
follow = switch.follow['switch']
cases = switch.cases
self.switch_follow.append(follow)
default = switch.default
for i, node in enumerate(cases):
if node in self.visited_nodes:
continue
cur_ks = switch.node_to_case[node][:]
if i + 1 < len(cases):
self.next_case = cases[i + 1]
else:
self.next_case = None
if node is default:
cur_ks.append(None)
default = None
with self as body:
self.visit_node(node)
if self.need_break:
self.add(jump_stmt('break'))
else:
self.need_break = True
ksv_pairs.append((cur_ks, body))
if default not in (None, follow):
with self as body:
self.visit_node(default)
ksv_pairs.append(([None], body))
self.add(switch_stmt(cond_expr, ksv_pairs))
self.switch_follow.pop()
self.visit_node(follow)
def visit_statement_node(self, stmt):
sucs = self.graph.sucs(stmt)
for ins in stmt.get_ins():
self.visit_ins(ins)
if len(sucs) == 1:
if sucs[0] is self.loop_follow[-1]:
self.add(jump_stmt('break'))
elif sucs[0] is self.next_case:
self.need_break = False
else:
self.visit_node(sucs[0])
def visit_try_node(self, try_node):
with self as tryb:
self.try_follow.append(try_node.follow)
self.visit_node(try_node.try_start)
pairs = []
for catch_node in try_node.catch:
if catch_node.exception_ins:
ins = catch_node.exception_ins
assert(isinstance(ins, instruction.MoveExceptionExpression))
var = ins.var_map[ins.ref]
var.declared = True
ctype = var.get_type()
name = 'v{}'.format(var.name)
else:
ctype = catch_node.catch_type
name = '_'
catch_decl = var_decl(parse_descriptor(ctype), local(name))
with self as body:
self.visit_node(catch_node.catch_start)
pairs.append((catch_decl, body))
self.add(try_stmt(tryb, pairs))
self.visit_node(self.try_follow.pop())
def visit_return_node(self, ret):
self.need_break = False
for ins in ret.get_ins():
self.visit_ins(ins)
def visit_throw_node(self, throw):
for ins in throw.get_ins():
self.visit_ins(ins)
|
kanpol/abugfinder
|
tools/modified/androguard/decompiler/dad/ast.py
|
Python
|
gpl-3.0
| 23,808
|
[
"VisIt"
] |
2d151b71d65eff58c39e59a2f5ca5995f4b0252c643c3100d7dbfe0e8b1095c2
|
#
# Copyright (C) 2011-2021 Greg Landrum and other RDKit contributors
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import base64
import copy
import warnings
from io import BytesIO
import IPython
from IPython.display import SVG
from rdkit import Chem
from rdkit.Chem import Draw, rdchem, rdChemReactions
from rdkit.Chem.Draw import rdMolDraw2D
if IPython.release.version < '0.11':
raise ImportError('this module requires at least v0.11 of IPython')
try:
import py3Dmol
_canUse3D = True
except ImportError:
_canUse3D = False
from PIL import Image
from PIL.PngImagePlugin import PngInfo
molSize = (450, 150)
highlightSubstructs = True
kekulizeStructures = True
highlightByReactant = False
ipython_useSVG = False
ipython_showProperties = True
ipython_maxProperties = 10
ipython_3d = False
molSize_3d = (400, 400)
drawing_type_3d = 'stick' # default drawing type for 3d structures
bgcolor_3d = '0xeeeeee'
drawOptions = rdMolDraw2D.MolDrawOptions()
def addMolToView(mol, view, confId=-1, drawAs=None):
if mol.GetNumAtoms() >= 999 or drawAs == 'cartoon':
# py3DMol is happier with TER and MASTER records present
pdb = Chem.MolToPDBBlock(mol, flavor=0x20 | 0x10)
view.addModel(pdb, 'pdb')
else:
# py3Dmol does not currently support v3k mol files, so
# we can only provide those with "smaller" molecules
mb = Chem.MolToMolBlock(mol, confId=confId)
view.addModel(mb, 'sdf')
if drawAs is None:
drawAs = drawing_type_3d
view.setStyle({drawAs: {}})
def drawMol3D(m, view=None, confId=-1, drawAs=None, bgColor=None, size=None):
if bgColor is None:
bgColor = bgcolor_3d
if size is None:
size = molSize_3d
if view is None:
view = py3Dmol.view(width=size[0], height=size[1])
view.removeAllModels()
try:
ms = iter(m)
for m in ms:
addMolToView(m, view, confId, drawAs)
except TypeError:
addMolToView(m, view, confId, drawAs)
view.setBackgroundColor(bgColor)
view.zoomTo()
return view.show()
def _toJSON(mol):
"""For IPython notebook, renders 3D webGL objects."""
if not ipython_3d or not mol.GetNumConformers():
return None
conf = mol.GetConformer()
if not conf.Is3D():
return None
res = drawMol3D(mol)
if hasattr(res, 'data'):
return res.data
return ""
def _toHTML(mol):
if _canUse3D and ipython_3d and mol.GetNumConformers():
return _toJSON(mol)
props = mol.GetPropsAsDict()
if not ipython_showProperties or not props:
return _toSVG(mol)
if mol.HasProp('_Name'):
nm = mol.GetProp('_Name')
else:
nm = ''
res = []
if not ipython_useSVG:
png = Draw._moltoimg(mol, molSize, [], nm, returnPNG=True, drawOptions=drawOptions)
png = base64.b64encode(png)
res.append(f'<tr><td colspan=2 style="text-align:center"><image src="data:image/png;base64,{png.decode()}"></td></tr>')
else:
svg = Draw._moltoSVG(mol, molSize, [], nm, kekulize=kekulizeStructures, drawOptions=drawOptions)
res.append(f'<tr><td colspan=2 style="text-align:center">{svg}</td></tr>')
for i,(pn, pv) in enumerate(props.items()):
if ipython_maxProperties >= 0 and i >= ipython_maxProperties:
res.append('<tr><td colspan=2 style="text-align:center">Property list truncated.<br />Increase IPythonConsole.ipython_maxProperties (or set it to -1) to see more properties.</td></tr>')
break
res.append(
f'<tr><th style="text-align:right">{pn}</th><td style="text-align:left">{pv}</td></tr>')
res = "\n".join(res)
return f'<table>{res}</table>'
def _toPNG(mol):
if hasattr(mol, '__sssAtoms'):
highlightAtoms = mol.__sssAtoms
else:
highlightAtoms = []
kekulize = kekulizeStructures
return Draw._moltoimg(mol, molSize, highlightAtoms, "", returnPNG=True, kekulize=kekulize,
drawOptions=drawOptions)
def _toSVG(mol):
if not ipython_useSVG:
return None
if hasattr(mol, '__sssAtoms'):
highlightAtoms = mol.__sssAtoms
else:
highlightAtoms = []
kekulize = kekulizeStructures
return Draw._moltoSVG(mol, molSize, highlightAtoms, "", kekulize, drawOptions=drawOptions)
def _toReactionPNG(rxn):
rc = copy.deepcopy(rxn)
return Draw.ReactionToImage(rc, subImgSize=(int(molSize[0] / 3), molSize[1]),
highlightByReactant=highlightByReactant, drawOptions=drawOptions,
returnPNG=True)
def _toReactionSVG(rxn):
if not ipython_useSVG:
return None
rc = copy.deepcopy(rxn)
return Draw.ReactionToImage(rc, subImgSize=(int(molSize[0] / 3), molSize[1]), useSVG=True,
highlightByReactant=highlightByReactant, drawOptions=drawOptions)
def _toMolBundlePNG(bundle):
if _MolsToGridImageSaved is not None:
fn = _MolsToGridImageSaved
else:
fn = Draw.MolsToGridImage
return fn(bundle, subImgSize=molSize, drawOptions=drawOptions, useSVG=False, returnPNG=True)
def _toMolBundleSVG(bundle):
if not ipython_useSVG:
return None
if _MolsToGridImageSaved is not None:
fn = _MolsToGridImageSaved
else:
fn = Draw.MolsToGridImage
return fn(bundle, subImgSize=molSize, drawOptions=drawOptions, useSVG=True)
def _GetSubstructMatch(mol, query, *args, **kwargs):
res = mol.__GetSubstructMatch(query, *args, **kwargs)
if highlightSubstructs:
mol.__sssAtoms = list(res)
else:
mol.__sssAtoms = []
return res
_GetSubstructMatch.__doc__ = rdchem.Mol.GetSubstructMatch.__doc__
def _GetSubstructMatches(mol, query, *args, **kwargs):
res = mol.__GetSubstructMatches(query, *args, **kwargs)
mol.__sssAtoms = []
if highlightSubstructs:
for entry in res:
mol.__sssAtoms.extend(list(entry))
return res
_GetSubstructMatches.__doc__ = rdchem.Mol.GetSubstructMatches.__doc__
# code for displaying PIL images directly,
def display_pil_image(img):
"""displayhook function for PIL Images, rendered as PNG"""
# pull metadata from the image, if there
metadata = PngInfo()
for k, v in img.info.items():
metadata.add_text(k, v)
bio = BytesIO()
img.save(bio, format='PNG', pnginfo=metadata)
return bio.getvalue()
_MolsToGridImageSaved = None
from IPython import display
def ShowMols(mols, maxMols=50, **kwargs):
global _MolsToGridImageSaved
if 'useSVG' not in kwargs:
kwargs['useSVG'] = ipython_useSVG
if 'returnPNG' not in kwargs:
kwargs['returnPNG'] = True
if _MolsToGridImageSaved is not None:
fn = _MolsToGridImageSaved
else:
fn = Draw.MolsToGridImage
if len(mols) > maxMols:
warnings.warn(
"Truncating the list of molecules to be displayed to %d. Change the maxMols value to display more."
% (maxMols))
mols = mols[:maxMols]
for prop in ('legends', 'highlightAtoms', 'highlightBonds'):
if prop in kwargs:
kwargs[prop] = kwargs[prop][:maxMols]
if "drawOptions" not in kwargs:
kwargs["drawOptions"] = drawOptions
res = fn(mols, **kwargs)
if kwargs['useSVG']:
return SVG(res)
if kwargs['returnPNG']:
return display.Image(data=res, format='png')
return res
ShowMols.__doc__ = Draw.MolsToGridImage.__doc__
def _DrawBit(fn, *args, **kwargs):
if 'useSVG' not in kwargs:
kwargs['useSVG'] = ipython_useSVG
res = fn(*args, **kwargs)
if kwargs['useSVG']:
return SVG(res)
sio = BytesIO(res)
return Image.open(sio)
def _DrawBits(fn, *args, **kwargs):
if 'useSVG' not in kwargs:
kwargs['useSVG'] = ipython_useSVG
res = fn(*args, **kwargs)
if kwargs['useSVG']:
return SVG(res)
sio = BytesIO(res)
return Image.open(sio)
_DrawMorganBitSaved = None
def DrawMorganBit(mol, bitId, bitInfo, drawOptions=drawOptions, **kwargs):
global _DrawMorganBitSaved
if _DrawMorganBitSaved is not None:
fn = _DrawMorganBitSaved
else:
fn = Draw.DrawMorganBit
return _DrawBit(fn, mol, bitId, bitInfo, drawOptions=drawOptions, **kwargs)
DrawMorganBit.__doc__ = Draw.DrawMorganBit.__doc__
_DrawMorganBitsSaved = None
def DrawMorganBits(*args, drawOptions=drawOptions, **kwargs):
global _DrawMorganBitsSaved
if _DrawMorganBitsSaved is not None:
fn = _DrawMorganBitsSaved
else:
fn = Draw.DrawMorganBits
return _DrawBit(fn, *args, drawOptions=drawOptions, **kwargs)
DrawMorganBits.__doc__ = Draw.DrawMorganBits.__doc__
_DrawRDKitBitSaved = None
def DrawRDKitBit(mol, bitId, bitInfo, drawOptions=drawOptions, **kwargs):
global _DrawRDKitBitSaved
if _DrawRDKitBitSaved is not None:
fn = _DrawRDKitBitSaved
else:
fn = Draw.DrawRDKitBit
return _DrawBit(fn, mol, bitId, bitInfo, drawOptions=drawOptions, **kwargs)
DrawRDKitBit.__doc__ = Draw.DrawRDKitBit.__doc__
_DrawRDKitBitsSaved = None
def DrawRDKitBits(*args, drawOptions=drawOptions, **kwargs):
global _DrawRDKitBitsSaved
if _DrawRDKitBitsSaved is not None:
fn = _DrawRDKitBitsSaved
else:
fn = Draw.DrawRDKitBits
return _DrawBit(fn, *args, drawOptions=drawOptions, **kwargs)
DrawRDKitBits.__doc__ = Draw.DrawRDKitBits.__doc__
_rendererInstalled = False
def EnableSubstructMatchRendering():
if not hasattr(rdchem.Mol, '__GetSubstructMatch'):
rdchem.Mol.__GetSubstructMatch = rdchem.Mol.GetSubstructMatch
rdchem.Mol.GetSubstructMatch = _GetSubstructMatch
if not hasattr(rdchem.Mol, '__GetSubstructMatches'):
rdchem.Mol.__GetSubstructMatches = rdchem.Mol.GetSubstructMatches
rdchem.Mol.GetSubstructMatches = _GetSubstructMatches
_methodsToDelete = []
def InstallIPythonRenderer():
global _MolsToGridImageSaved, _DrawRDKitBitSaved, _DrawRDKitBitsSaved, _DrawMorganBitSaved, _DrawMorganBitsSaved
global _rendererInstalled
if _rendererInstalled:
return
rdchem.Mol._repr_png_ = _toPNG
rdchem.Mol._repr_svg_ = _toSVG
_methodsToDelete.append((rdchem.Mol, '_repr_png_'))
_methodsToDelete.append((rdchem.Mol, '_repr_svg_'))
rdchem.Mol._repr_html_ = _toHTML
_methodsToDelete.append((rdchem.Mol, '_repr_html_'))
rdChemReactions.ChemicalReaction._repr_png_ = _toReactionPNG
rdChemReactions.ChemicalReaction._repr_svg_ = _toReactionSVG
_methodsToDelete.append((rdChemReactions.ChemicalReaction, '_repr_png_'))
_methodsToDelete.append((rdChemReactions.ChemicalReaction, '_repr_svg_'))
rdchem.MolBundle._repr_png_ = _toMolBundlePNG
rdchem.MolBundle._repr_svg_ = _toMolBundleSVG
_methodsToDelete.append((rdchem.MolBundle, '_repr_png_'))
_methodsToDelete.append((rdchem.MolBundle, '_repr_svg_'))
EnableSubstructMatchRendering()
Image.Image._repr_png_ = display_pil_image
_methodsToDelete.append((Image.Image, '_repr_png_'))
_MolsToGridImageSaved = Draw.MolsToGridImage
Draw.MolsToGridImage = ShowMols
_DrawRDKitBitSaved = Draw.DrawRDKitBit
Draw.DrawRDKitBit = DrawRDKitBit
_DrawRDKitBitsSaved = Draw.DrawRDKitBits
Draw.DrawRDKitBits = DrawRDKitBits
_DrawMorganBitSaved = Draw.DrawMorganBit
Draw.DrawMorganBit = DrawMorganBit
_DrawMorganBitsSaved = Draw.DrawMorganBits
Draw.DrawMorganBits = DrawMorganBits
rdchem.Mol.__DebugMol = rdchem.Mol.Debug
rdchem.Mol.Debug = lambda self, useStdout=False: self.__DebugMol(useStdout=useStdout)
_rendererInstalled = True
InstallIPythonRenderer()
def DisableSubstructMatchRendering():
if hasattr(rdchem.Mol, '__GetSubstructMatch'):
rdchem.Mol.GetSubstructMatch = rdchem.Mol.__GetSubstructMatch
del rdchem.Mol.__GetSubstructMatch
if hasattr(rdchem.Mol, '__GetSubstructMatches'):
rdchem.Mol.GetSubstructMatches = rdchem.Mol.__GetSubstructMatches
del rdchem.Mol.__GetSubstructMatches
def UninstallIPythonRenderer():
global _MolsToGridImageSaved, _DrawRDKitBitSaved, _DrawMorganBitSaved, _DrawMorganBitsSaved
global _rendererInstalled, _methodsToDelete
if not _rendererInstalled:
return
for cls, attr in _methodsToDelete:
delattr(cls, attr)
_methodsToDelete = []
DisableSubstructMatchRendering()
if _MolsToGridImageSaved is not None:
Draw.MolsToGridImage = _MolsToGridImageSaved
if _DrawRDKitBitSaved is not None:
Draw.DrawRDKitBit = _DrawRDKitBitSaved
if _DrawRDKitBitsSaved is not None:
Draw.DrawRDKitBits = _DrawRDKitBitsSaved
if _DrawMorganBitSaved is not None:
Draw.DrawMorganBit = _DrawMorganBitSaved
if _DrawMorganBitsSaved is not None:
Draw.DrawMorganBits = _DrawMorganBitsSaved
if hasattr(rdchem.Mol, '__DebugMol'):
rdchem.Mol.Debug = rdchem.Mol.__DebugMol
del rdchem.Mol.__DebugMol
_rendererInstalled = False
|
rdkit/rdkit
|
rdkit/Chem/Draw/IPythonConsole.py
|
Python
|
bsd-3-clause
| 12,511
|
[
"RDKit"
] |
51d840e226799ce027df635792db3006f150e81652615a7a5ec99b68265f3f2e
|
from setuptools import setup, find_packages
from pip.req import parse_requirements
install_reqs = parse_requirements('requirements.txt', session=False)
version = '0.2.5'
LONG_DESCRIPTION = """
=====
Zops
=====
Zops - Utils for devops teams that want to deploy using Zappa
"""
setup(
name='zops',
version=version,
description="""Utils for devops teams that want to deploy using Zappa""",
long_description=LONG_DESCRIPTION,
classifiers=[
"Programming Language :: Python",
"Topic :: Software Development :: Libraries :: Python Modules",
"Environment :: Web Environment",
],
keywords='zappa, aws, lambda',
author='Brian Jinwright',
author_email='opensource@ipoots.com',
maintainer='Brian Jinwright',
packages=find_packages(),
py_modules=['zops.cli'],
entry_points='''
[console_scripts]
zops=zops.cli:zops_ins
''',
license='GNU GPL V3',
install_requires=[str(ir.req) for ir in install_reqs],
include_package_data=True,
zip_safe=False,
)
|
bjinwright/zops
|
setup.py
|
Python
|
gpl-3.0
| 1,042
|
[
"Brian"
] |
5bb349830b4d3992a72ca6b28401944a94c475e3995b6eb84d8df705c6b1add8
|
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains classes to wrap Python VTK to make nice molecular plots.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Nov 27, 2011"
import os
import itertools
import math
import subprocess
import time
import numpy as np
try:
import vtk
from vtk import vtkInteractorStyleTrackballCamera
except ImportError:
# VTK not present. The Camera is to set object to avoid errors in unittest.
vtk = None
vtkInteractorStyleTrackballCamera = object
from monty.serialization import loadfn
from monty.dev import requires
from pymatgen.util.coord import in_coord_list
from pymatgen.core.periodic_table import Specie
from pymatgen.core.structure import Structure
from pymatgen.core.sites import PeriodicSite
module_dir = os.path.dirname(os.path.abspath(__file__))
EL_COLORS = loadfn(os.path.join(module_dir, "ElementColorSchemes.yaml"))
class StructureVis(object):
"""
Provides Structure object visualization using VTK.
"""
@requires(vtk, "Visualization requires the installation of VTK with "
"Python bindings.")
def __init__(self, element_color_mapping=None, show_unit_cell=True,
show_bonds=False, show_polyhedron=True,
poly_radii_tol_factor=0.5, excluded_bonding_elements=None):
"""
Constructs a Structure Visualization.
Args:
element_color_mapping: Optional color mapping for the elements,
as a dict of {symbol: rgb tuple}. For example, {"Fe": (255,
123,0), ....} If None is specified, a default based on
Jmol"s color scheme is used.
show_unit_cell: Set to False to not show the unit cell
boundaries. Defaults to True.
show_bonds: Set to True to show bonds. Defaults to True.
show_polyhedron: Set to True to show polyhedrons. Defaults to
False.
poly_radii_tol_factor: The polyhedron and bonding code uses the
ionic radii of the elements or species to determine if two
atoms are bonded. This specifies a tolerance scaling factor
such that atoms which are (1 + poly_radii_tol_factor) * sum
of ionic radii apart are still considered as bonded.
excluded_bonding_elements: List of atom types to exclude from
bonding determination. Defaults to an empty list. Useful
when trying to visualize a certain atom type in the
framework (e.g., Li in a Li-ion battery cathode material).
Useful keyboard shortcuts implemented.
h : Show help
A/a : Increase/decrease cell by one unit vector in a-direction
B/b : Increase/decrease cell by one unit vector in b-direction
C/c : Increase/decrease cell by one unit vector in c-direction
# : Toggle showing of polyhedrons
- : Toggle showing of bonds
[ : Decrease poly_radii_tol_factor by 0.05
] : Increase poly_radii_tol_factor by 0.05
r : Reset camera direction
o : Orthogonalize structure
Up/Down : Rotate view along Up direction by 90 clock/anticlockwise
Left/right : Rotate view along camera direction by 90
clock/anticlockwise
"""
# create a rendering window and renderer
self.ren = vtk.vtkRenderer()
self.ren_win = vtk.vtkRenderWindow()
self.ren_win.AddRenderer(self.ren)
self.ren.SetBackground(1, 1, 1)
self.title = "Structure Visualizer"
# create a renderwindowinteractor
self.iren = vtk.vtkRenderWindowInteractor()
self.iren.SetRenderWindow(self.ren_win)
self.mapper_map = {}
self.structure = None
if element_color_mapping:
self.el_color_mapping = element_color_mapping
else:
self.el_color_mapping = EL_COLORS["VESTA"]
self.show_unit_cell = show_unit_cell
self.show_bonds = show_bonds
self.show_polyhedron = show_polyhedron
self.poly_radii_tol_factor = poly_radii_tol_factor
self.excluded_bonding_elements = excluded_bonding_elements if \
excluded_bonding_elements else []
self.show_help = True
self.supercell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
self.redraw()
style = StructureInteractorStyle(self)
self.iren.SetInteractorStyle(style)
self.ren.parent = self
def rotate_view(self, axis_ind=0, angle=0):
"""
Rotate the camera view.
Args:
axis_ind: Index of axis to rotate. Defaults to 0, i.e., a-axis.
angle: Angle to rotate by. Defaults to 0.
"""
camera = self.ren.GetActiveCamera()
if axis_ind == 0:
camera.Roll(angle)
elif axis_ind == 1:
camera.Azimuth(angle)
else:
camera.Pitch(angle)
self.ren_win.Render()
def write_image(self, filename="image.png", magnification=1,
image_format="png"):
"""
Save render window to an image.
Arguments:
filename:
filename to save to. Defaults to image.png.
magnification:
magnification. Use it to render high res images.
image_format:
choose between jpeg, png. Png is the default.
"""
render_large = vtk.vtkRenderLargeImage()
render_large.SetInput(self.ren)
if image_format == "jpeg":
writer = vtk.vtkJPEGWriter()
writer.SetQuality(80)
else:
writer = vtk.vtkPNGWriter()
render_large.SetMagnification(magnification)
writer.SetFileName(filename)
writer.SetInputConnection(render_large.GetOutputPort())
self.ren_win.Render()
writer.Write()
del render_large
def redraw(self, reset_camera=False):
"""
Redraw the render window.
Args:
reset_camera: Set to True to reset the camera to a
pre-determined default for each structure. Defaults to False.
"""
self.ren.RemoveAllViewProps()
self.picker = None
self.add_picker_fixed()
self.helptxt_mapper = vtk.vtkTextMapper()
tprops = self.helptxt_mapper.GetTextProperty()
tprops.SetFontSize(14)
tprops.SetFontFamilyToTimes()
tprops.SetColor(0, 0, 0)
if self.structure is not None:
self.set_structure(self.structure, reset_camera)
self.ren_win.Render()
def orthongonalize_structure(self):
if self.structure is not None:
self.set_structure(self.structure.copy(sanitize=True))
self.ren_win.Render()
def display_help(self):
"""
Display the help for various keyboard shortcuts.
"""
helptxt = ["h : Toggle help",
"A/a, B/b or C/c : Increase/decrease cell by one a,"
" b or c unit vector", "# : Toggle showing of polyhedrons",
"-: Toggle showing of bonds", "r : Reset camera direction",
"[/]: Decrease or increase poly_radii_tol_factor "
"by 0.05. Value = " + str(self.poly_radii_tol_factor),
"Up/Down: Rotate view along Up direction by 90 "
"clockwise/anticlockwise",
"Left/right: Rotate view along camera direction by "
"90 clockwise/anticlockwise", "s: Save view to image.png",
"o: Orthogonalize structure"]
self.helptxt_mapper.SetInput("\n".join(helptxt))
self.helptxt_actor.SetPosition(10, 10)
self.helptxt_actor.VisibilityOn()
def set_structure(self, structure, reset_camera=True, to_unit_cell=True):
"""
Add a structure to the visualizer.
Args:
structure: structure to visualize
reset_camera: Set to True to reset the camera to a default
determined based on the structure.
to_unit_cell: Whether or not to fall back sites into the unit cell.
"""
self.ren.RemoveAllViewProps()
has_lattice = hasattr(structure, "lattice")
if has_lattice:
s = Structure.from_sites(structure, to_unit_cell=to_unit_cell)
s.make_supercell(self.supercell, to_unit_cell=to_unit_cell)
else:
s = structure
inc_coords = []
for site in s:
self.add_site(site)
inc_coords.append(site.coords)
count = 0
labels = ["a", "b", "c"]
colors = [(1, 0, 0), (0, 1, 0), (0, 0, 1)]
if has_lattice:
matrix = s.lattice.matrix
if self.show_unit_cell and has_lattice:
#matrix = s.lattice.matrix
self.add_text([0, 0, 0], "o")
for vec in matrix:
self.add_line((0, 0, 0), vec, colors[count])
self.add_text(vec, labels[count], colors[count])
count += 1
for (vec1, vec2) in itertools.permutations(matrix, 2):
self.add_line(vec1, vec1 + vec2)
for (vec1, vec2, vec3) in itertools.permutations(matrix, 3):
self.add_line(vec1 + vec2, vec1 + vec2 + vec3)
if self.show_bonds or self.show_polyhedron:
elements = sorted(s.composition.elements, key=lambda a: a.X)
anion = elements[-1]
def contains_anion(site):
for sp in site.species_and_occu.keys():
if sp.symbol == anion.symbol:
return True
return False
anion_radius = anion.average_ionic_radius
for site in s:
exclude = False
max_radius = 0
color = np.array([0, 0, 0])
for sp, occu in site.species_and_occu.items():
if sp.symbol in self.excluded_bonding_elements \
or sp == anion:
exclude = True
break
max_radius = max(max_radius, sp.average_ionic_radius)
color = color + \
occu * np.array(self.el_color_mapping.get(sp.symbol,
[0, 0, 0]))
if not exclude:
max_radius = (1 + self.poly_radii_tol_factor) * \
(max_radius + anion_radius)
nn = structure.get_neighbors(site, float(max_radius))
nn_sites = []
for nnsite, dist in nn:
if contains_anion(nnsite):
nn_sites.append(nnsite)
if not in_coord_list(inc_coords, nnsite.coords):
self.add_site(nnsite)
if self.show_bonds:
self.add_bonds(nn_sites, site)
if self.show_polyhedron:
color = [i / 255 for i in color]
self.add_polyhedron(nn_sites, site, color)
if self.show_help:
self.helptxt_actor = vtk.vtkActor2D()
self.helptxt_actor.VisibilityOn()
self.helptxt_actor.SetMapper(self.helptxt_mapper)
self.ren.AddActor(self.helptxt_actor)
self.display_help()
camera = self.ren.GetActiveCamera()
if reset_camera:
if has_lattice:
#Adjust the camera for best viewing
lengths = s.lattice.abc
pos = (matrix[1] + matrix[2]) * 0.5 + \
matrix[0] * max(lengths) / lengths[0] * 3.5
camera.SetPosition(pos)
camera.SetViewUp(matrix[2])
camera.SetFocalPoint((matrix[0] + matrix[1] + matrix[2]) * 0.5)
else:
origin = s.center_of_mass
max_site = max(
s, key=lambda site: site.distance_from_point(origin))
camera.SetPosition(origin + 5 * (max_site.coords - origin))
camera.SetFocalPoint(s.center_of_mass)
self.structure = structure
self.title = s.composition.formula
def zoom(self, factor):
"""
Zoom the camera view by a factor.
"""
camera = self.ren.GetActiveCamera()
camera.Zoom(factor)
self.ren_win.Render()
def show(self):
"""
Display the visualizer.
"""
self.iren.Initialize()
self.ren_win.SetSize(800, 800)
self.ren_win.SetWindowName(self.title)
self.ren_win.Render()
self.iren.Start()
def add_site(self, site):
"""
Add a site to the render window. The site is displayed as a sphere, the
color of which is determined based on the element. Partially occupied
sites are displayed as a single element color, though the site info
still shows the partial occupancy.
Args:
site: Site to add.
"""
start_angle = 0
radius = 0
total_occu = 0
for specie, occu in site.species_and_occu.items():
radius += occu * (specie.ionic_radius
if isinstance(specie, Specie)
and specie.ionic_radius
else specie.average_ionic_radius)
total_occu += occu
vis_radius = 0.2 + 0.002 * radius
for specie, occu in site.species_and_occu.items():
if not specie:
color = (1, 1, 1)
elif specie.symbol in self.el_color_mapping:
color = [i / 255 for i in self.el_color_mapping[specie.symbol]]
mapper = self.add_partial_sphere(site.coords, vis_radius, color,
start_angle, start_angle + 360 * occu)
self.mapper_map[mapper] = [site]
start_angle += 360 * occu
if total_occu < 1:
mapper = self.add_partial_sphere(site.coords, vis_radius, (1,1,1),
start_angle, start_angle + 360 * (1 - total_occu))
self.mapper_map[mapper] = [site]
def add_partial_sphere(self, coords, radius, color, start=0, end=360,
opacity=1.0):
sphere = vtk.vtkSphereSource()
sphere.SetCenter(coords)
sphere.SetRadius(radius)
sphere.SetThetaResolution(18)
sphere.SetPhiResolution(18)
sphere.SetStartTheta(start)
sphere.SetEndTheta(end)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(sphere.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(color)
actor.GetProperty().SetOpacity(opacity)
self.ren.AddActor(actor)
return mapper
def add_text(self, coords, text, color=(0, 0, 0)):
"""
Add text at a coordinate.
Args:
coords: Coordinates to add text at.
text: Text to place.
color: Color for text as RGB. Defaults to black.
"""
source = vtk.vtkVectorText()
source.SetText(text)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(source.GetOutputPort())
follower = vtk.vtkFollower()
follower.SetMapper(mapper)
follower.GetProperty().SetColor(color)
follower.SetPosition(coords)
follower.SetScale(0.5)
self.ren.AddActor(follower)
follower.SetCamera(self.ren.GetActiveCamera())
def add_line(self, start, end, color=(0.5, 0.5, 0.5), width=1):
"""
Adds a line.
Args:
start: Starting coordinates for line.
end: Ending coordinates for line.
color: Color for text as RGB. Defaults to grey.
width: Width of line. Defaults to 1.
"""
source = vtk.vtkLineSource()
source.SetPoint1(start)
source.SetPoint2(end)
vertexIDs = vtk.vtkStringArray()
vertexIDs.SetNumberOfComponents(1)
vertexIDs.SetName("VertexIDs")
# Set the vertex labels
vertexIDs.InsertNextValue("a")
vertexIDs.InsertNextValue("b")
source.GetOutput().GetPointData().AddArray(vertexIDs)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(source.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(color)
actor.GetProperty().SetLineWidth(width)
self.ren.AddActor(actor)
def add_polyhedron(self, neighbors, center, color, opacity=1.0,
draw_edges=False, edges_color=[0.0, 0.0, 0.0],
edges_linewidth=2):
"""
Adds a polyhedron.
Args:
neighbors: Neighbors of the polyhedron (the vertices).
center: The atom in the center of the polyhedron.
color: Color for text as RGB.
opacity: Opacity of the polyhedron
draw_edges: If set to True, the a line will be drawn at each edge
edges_color: Color of the line for the edges
edges_linewidth: Width of the line drawn for the edges
"""
points = vtk.vtkPoints()
conv = vtk.vtkConvexPointSet()
for i in range(len(neighbors)):
x, y, z = neighbors[i].coords
points.InsertPoint(i, x, y, z)
conv.GetPointIds().InsertId(i, i)
grid = vtk.vtkUnstructuredGrid()
grid.Allocate(1, 1)
grid.InsertNextCell(conv.GetCellType(), conv.GetPointIds())
grid.SetPoints(points)
dsm = vtk.vtkDataSetMapper()
polysites = [center]
polysites.extend(neighbors)
self.mapper_map[dsm] = polysites
if vtk.VTK_MAJOR_VERSION <= 5:
dsm.SetInputConnection(grid.GetProducerPort())
else:
dsm.SetInputData(grid)
ac = vtk.vtkActor()
#ac.SetMapper(mapHull)
ac.SetMapper(dsm)
ac.GetProperty().SetOpacity(opacity)
if color == 'element':
# If partial occupations are involved, the color of the specie with
# the highest occupation is used
myoccu = 0.0
for specie, occu in center.species_and_occu.items():
if occu > myoccu:
myspecie = specie
myoccu = occu
color = [i / 255 for i in self.el_color_mapping[myspecie.symbol]]
ac.GetProperty().SetColor(color)
else:
ac.GetProperty().SetColor(color)
if draw_edges:
ac.GetProperty().SetEdgeColor(edges_color)
ac.GetProperty().SetLineWidth(edges_linewidth)
ac.GetProperty().EdgeVisibilityOn()
self.ren.AddActor(ac)
def add_triangle(self, neighbors, color, center=None, opacity=0.4,
draw_edges=False, edges_color=[0.0, 0.0, 0.0],
edges_linewidth=2):
"""
Adds a triangular surface between three atoms.
Args:
atoms: Atoms between which a triangle will be drawn.
color: Color for triangle as RGB.
center: The "central atom" of the triangle
opacity: opacity of the triangle
draw_edges: If set to True, the a line will be drawn at each edge
edges_color: Color of the line for the edges
edges_linewidth: Width of the line drawn for the edges
"""
points = vtk.vtkPoints()
triangle = vtk.vtkTriangle()
for ii in range(3):
points.InsertNextPoint(neighbors[ii].x, neighbors[ii].y,
neighbors[ii].z)
triangle.GetPointIds().SetId(ii, ii)
triangles = vtk.vtkCellArray()
triangles.InsertNextCell(triangle)
# polydata object
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints( points )
trianglePolyData.SetPolys( triangles )
# mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(trianglePolyData)
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
if color == 'element':
if center is None:
raise ValueError(
'Color should be chosen according to the central atom, '
'and central atom is not provided')
# If partial occupations are involved, the color of the specie with
# the highest occupation is used
myoccu = 0.0
for specie, occu in center.species_and_occu.items():
if occu > myoccu:
myspecie = specie
myoccu = occu
color = [i / 255 for i in self.el_color_mapping[myspecie.symbol]]
ac.GetProperty().SetColor(color)
else:
ac.GetProperty().SetColor(color)
if draw_edges:
ac.GetProperty().SetEdgeColor(edges_color)
ac.GetProperty().SetLineWidth(edges_linewidth)
ac.GetProperty().EdgeVisibilityOn()
self.ren.AddActor(ac)
def add_faces(self, faces, color, opacity=0.35):
for face in faces:
if len(face) == 3:
points = vtk.vtkPoints()
triangle = vtk.vtkTriangle()
for ii in range(3):
points.InsertNextPoint(face[ii][0], face[ii][1], face[ii][2])
triangle.GetPointIds().SetId(ii, ii)
triangles = vtk.vtkCellArray()
triangles.InsertNextCell(triangle)
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints(points)
trianglePolyData.SetPolys(triangles)
mapper = vtk.vtkPolyDataMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
mapper.SetInputConnection(trianglePolyData.GetProducerPort())
else:
mapper.SetInputData(trianglePolyData)
# mapper.SetInput(trianglePolyData)
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
elif False and len(face) == 4:
points = vtk.vtkPoints()
for ii in range(4):
points.InsertNextPoint(face[ii][0], face[ii][1], face[ii][2])
line1 = vtk.vtkLine()
line1.GetPointIds().SetId(0, 0)
line1.GetPointIds().SetId(1, 2)
line2 = vtk.vtkLine()
line2.GetPointIds().SetId(0, 3)
line2.GetPointIds().SetId(1, 1)
lines = vtk.vtkCellArray()
lines.InsertNextCell(line1)
lines.InsertNextCell(line2)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetLines(lines)
ruledSurfaceFilter = vtk.vtkRuledSurfaceFilter()
ruledSurfaceFilter.SetInput(polydata)
ruledSurfaceFilter.SetResolution(15, 15)
ruledSurfaceFilter.SetRuledModeToResample()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(ruledSurfaceFilter.GetOutput())
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
elif len(face) > 3:
center = np.zeros(3, np.float)
for site in face:
center += site
center /= np.float(len(face))
for ii in range(len(face)):
points = vtk.vtkPoints()
triangle = vtk.vtkTriangle()
points.InsertNextPoint(face[ii][0], face[ii][1], face[ii][2])
ii2 = np.mod(ii+1, len(face))
points.InsertNextPoint(face[ii2][0], face[ii2][1], face[ii2][2])
points.InsertNextPoint(center[0], center[1], center[2])
for ii in range(3):
triangle.GetPointIds().SetId(ii, ii)
triangles = vtk.vtkCellArray()
triangles.InsertNextCell(triangle)
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints(points)
trianglePolyData.SetPolys(triangles)
mapper = vtk.vtkPolyDataMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
mapper.SetInputConnection(trianglePolyData.GetProducerPort())
else:
mapper.SetInputData(trianglePolyData)
# mapper.SetInput(trianglePolyData)
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
else:
raise ValueError("Number of points for a face should be >= 3")
def add_edges(self, edges, type='line', linewidth=2, color=[0.0, 0.0, 0.0]):
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
for iedge, edge in enumerate(edges):
points.InsertPoint(2*iedge, edge[0])
points.InsertPoint(2*iedge + 1, edge[1])
lines.InsertNextCell(2)
lines.InsertCellPoint(2*iedge)
lines.InsertCellPoint(2*iedge + 1)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetLines(lines)
mapper = vtk.vtkPolyDataMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
mapper.SetInputConnection(polydata.GetProducerPort())
else:
mapper.SetInputData(polydata)
# mapper.SetInput(polydata)
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetColor(color)
ac.GetProperty().SetLineWidth(linewidth)
self.ren.AddActor(ac)
def add_bonds(self, neighbors, center, color=None, opacity=None,
radius=0.1):
"""
Adds bonds for a site.
Args:
neighbors: Neighbors of the site.
center: The site in the center for all bonds.
color: Color of the tubes representing the bonds
opacity: Opacity of the tubes representing the bonds
radius: Radius of tube s representing the bonds
"""
points = vtk.vtkPoints()
points.InsertPoint(0, center.x, center.y, center.z)
n = len(neighbors)
lines = vtk.vtkCellArray()
for i in range(n):
points.InsertPoint(i + 1, neighbors[i].coords)
lines.InsertNextCell(2)
lines.InsertCellPoint(0)
lines.InsertCellPoint(i + 1)
pd = vtk.vtkPolyData()
pd.SetPoints(points)
pd.SetLines(lines)
tube = vtk.vtkTubeFilter()
if vtk.VTK_MAJOR_VERSION <= 5:
tube.SetInputConnection(pd.GetProducerPort())
else:
tube.SetInputData(pd)
tube.SetRadius(radius)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(tube.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
if opacity is not None:
actor.GetProperty().SetOpacity(opacity)
if color is not None:
actor.GetProperty().SetColor(color)
self.ren.AddActor(actor)
def add_picker_fixed(self):
# Create a cell picker.
picker = vtk.vtkCellPicker()
# Create a Python function to create the text for the text mapper used
# to display the results of picking.
def annotate_pick(obj, event):
if picker.GetCellId() < 0 and not self.show_help:
self.helptxt_actor.VisibilityOff()
else:
mapper = picker.GetMapper()
if mapper in self.mapper_map:
output = []
for site in self.mapper_map[mapper]:
row = ["{} - ".format(site.species_string),
", ".join(["{:.3f}".format(c)
for c in site.frac_coords]),
"[" + ", ".join(["{:.3f}".format(c)
for c in site.coords]) +
"]"]
output.append("".join(row))
self.helptxt_mapper.SetInput("\n".join(output))
self.helptxt_actor.SetPosition(10, 10)
self.helptxt_actor.VisibilityOn()
self.show_help = False
self.picker = picker
picker.AddObserver("EndPickEvent", annotate_pick)
self.iren.SetPicker(picker)
def add_picker(self):
# Create a cell picker.
picker = vtk.vtkCellPicker()
# Create a Python function to create the text for the text mapper used
# to display the results of picking.
source = vtk.vtkVectorText()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(source.GetOutputPort())
follower = vtk.vtkFollower()
follower.SetMapper(mapper)
follower.GetProperty().SetColor((0, 0, 0))
follower.SetScale(0.2)
self.ren.AddActor(follower)
follower.SetCamera(self.ren.GetActiveCamera())
follower.VisibilityOff()
def annotate_pick(obj, event):
if picker.GetCellId() < 0:
follower.VisibilityOff()
else:
pick_pos = picker.GetPickPosition()
mapper = picker.GetMapper()
if mapper in self.mapper_map:
site = self.mapper_map[mapper]
output = [site.species_string, "Frac. coords: " +
" ".join(["{:.4f}".format(c)
for c in
site.frac_coords])]
source.SetText("\n".join(output))
follower.SetPosition(pick_pos)
follower.VisibilityOn()
picker.AddObserver("EndPickEvent", annotate_pick)
self.picker = picker
self.iren.SetPicker(picker)
class StructureInteractorStyle(vtkInteractorStyleTrackballCamera):
"""
A custom interactor style for visualizing structures.
"""
def __init__(self, parent):
self.parent = parent
self.AddObserver("LeftButtonPressEvent", self.leftButtonPressEvent)
self.AddObserver("MouseMoveEvent", self.mouseMoveEvent)
self.AddObserver("LeftButtonReleaseEvent", self.leftButtonReleaseEvent)
self.AddObserver("KeyPressEvent", self.keyPressEvent)
def leftButtonPressEvent(self, obj, event):
self.mouse_motion = 0
self.OnLeftButtonDown()
return
def mouseMoveEvent(self, obj, event):
self.mouse_motion = 1
self.OnMouseMove()
return
def leftButtonReleaseEvent(self, obj, event):
ren = obj.GetCurrentRenderer()
iren = ren.GetRenderWindow().GetInteractor()
if self.mouse_motion == 0:
pos = iren.GetEventPosition()
iren.GetPicker().Pick(pos[0], pos[1], 0, ren)
self.OnLeftButtonUp()
return
def keyPressEvent(self, obj, event):
parent = obj.GetCurrentRenderer().parent
sym = parent.iren.GetKeySym()
if sym in "ABCabc":
if sym == "A":
parent.supercell[0][0] += 1
elif sym == "B":
parent.supercell[1][1] += 1
elif sym == "C":
parent.supercell[2][2] += 1
elif sym == "a":
parent.supercell[0][0] = max(parent.supercell[0][0] - 1, 1)
elif sym == "b":
parent.supercell[1][1] = max(parent.supercell[1][1] - 1, 1)
elif sym == "c":
parent.supercell[2][2] = max(parent.supercell[2][2] - 1, 1)
parent.redraw()
elif sym == "numbersign":
parent.show_polyhedron = not parent.show_polyhedron
parent.redraw()
elif sym == "minus":
parent.show_bonds = not parent.show_bonds
parent.redraw()
elif sym == "bracketleft":
parent.poly_radii_tol_factor -= 0.05 \
if parent.poly_radii_tol_factor > 0 else 0
parent.redraw()
elif sym == "bracketright":
parent.poly_radii_tol_factor += 0.05
parent.redraw()
elif sym == "h":
parent.show_help = not parent.show_help
parent.redraw()
elif sym == "r":
parent.redraw(True)
elif sym == "s":
parent.write_image("image.png")
elif sym == "Up":
parent.rotate_view(1, 90)
elif sym == "Down":
parent.rotate_view(1, -90)
elif sym == "Left":
parent.rotate_view(0, -90)
elif sym == "Right":
parent.rotate_view(0, 90)
elif sym == "o":
parent.orthongonalize_structure()
parent.redraw()
self.OnKeyPress()
def make_movie(structures, output_filename="movie.mp4", zoom=1.0, fps=20,
bitrate="10000k", quality=1, **kwargs):
"""
Generate a movie from a sequence of structures using vtk and ffmpeg.
Args:
structures ([Structure]): sequence of structures
output_filename (str): filename for structure output. defaults to
movie.mp4
zoom (float): A zoom to be applied to the visualizer. Defaults to 1.0.
fps (int): Frames per second for the movie. Defaults to 20.
bitrate (str): Video bitate. Defaults to "10000k" (fairly high
quality).
quality (int): A quality scale. Defaults to 1.
\\*\\*kwargs: Any kwargs supported by StructureVis to modify the images
generated.
"""
vis = StructureVis(**kwargs)
vis.show_help = False
vis.redraw()
vis.zoom(zoom)
sigfig = int(math.floor(math.log10(len(structures))) + 1)
filename = "image{0:0" + str(sigfig) + "d}.png"
for i, s in enumerate(structures):
vis.set_structure(s)
vis.write_image(filename.format(i), 3)
filename = "image%0" + str(sigfig) + "d.png"
args = ["ffmpeg", "-y", "-i", filename,
"-q:v", str(quality), "-r", str(fps), "-b:v", str(bitrate),
output_filename]
subprocess.Popen(args)
class MultiStructuresVis(StructureVis):
DEFAULT_ANIMATED_MOVIE_OPTIONS = {'time_between_frames': 0.1,
'looping_type': 'restart',
'number_of_loops': 1,
'time_between_loops': 1.0}
def __init__(self, element_color_mapping=None, show_unit_cell=True,
show_bonds=False, show_polyhedron=False,
poly_radii_tol_factor=0.5, excluded_bonding_elements=None,
animated_movie_options=DEFAULT_ANIMATED_MOVIE_OPTIONS):
super(MultiStructuresVis, self).__init__(element_color_mapping=element_color_mapping,
show_unit_cell=show_unit_cell,
show_bonds=show_bonds, show_polyhedron=show_polyhedron,
poly_radii_tol_factor=poly_radii_tol_factor,
excluded_bonding_elements=excluded_bonding_elements)
self.warningtxt_actor = vtk.vtkActor2D()
self.infotxt_actor = vtk.vtkActor2D()
self.structures = None
style = MultiStructuresInteractorStyle(self)
self.iren.SetInteractorStyle(style)
self.istruct = 0
self.current_structure = None
self.set_animated_movie_options(animated_movie_options=animated_movie_options)
def set_structures(self, structures, tags=None):
self.structures = structures
self.istruct = 0
self.current_structure = self.structures[self.istruct]
self.tags = tags if tags is not None else []
self.all_radii = []
self.all_vis_radii = []
for struct in self.structures:
struct_radii = []
struct_vis_radii = []
for site in struct:
radius = 0
for specie, occu in site.species_and_occu.items():
radius += occu * (specie.ionic_radius
if isinstance(specie, Specie)
and specie.ionic_radius
else specie.average_ionic_radius)
vis_radius = 0.2 + 0.002 * radius
struct_radii.append(radius)
struct_vis_radii.append(vis_radius)
self.all_radii.append(struct_radii)
self.all_vis_radii.append(struct_vis_radii)
self.set_structure(self.current_structure, reset_camera=True, to_unit_cell=False)
def set_structure(self, structure, reset_camera=True, to_unit_cell=False):
super(MultiStructuresVis, self).set_structure(structure=structure, reset_camera=reset_camera,
to_unit_cell=to_unit_cell)
self.apply_tags()
def apply_tags(self):
tags = {}
for tag in self.tags:
istruct = tag.get('istruct', 'all')
if istruct != 'all':
if istruct != self.istruct:
continue
site_index = tag['site_index']
color = tag.get('color', [0.5, 0.5, 0.5])
opacity = tag.get('opacity', 0.5)
if site_index == 'unit_cell_all':
struct_radii = self.all_vis_radii[self.istruct]
for isite, site in enumerate(self.current_structure):
vis_radius = 1.5 * tag.get('radius', struct_radii[isite])
tags[(isite, (0, 0, 0))] = {'radius': vis_radius,
'color': color,
'opacity': opacity}
continue
cell_index = tag['cell_index']
if 'radius' in tag:
vis_radius = tag['radius']
elif 'radius_factor' in tag:
vis_radius = tag['radius_factor'] * self.all_vis_radii[self.istruct][site_index]
else:
vis_radius = 1.5 * self.all_vis_radii[self.istruct][site_index]
tags[(site_index, cell_index)] = {'radius': vis_radius,
'color': color,
'opacity': opacity}
for site_and_cell_index, tag_style in tags.items():
isite, cell_index = site_and_cell_index
site = self.current_structure[isite]
if cell_index == (0, 0, 0):
coords = site.coords
else:
fcoords = site.frac_coords + np.array(cell_index)
site_image = PeriodicSite(site.species_and_occu, fcoords,
self.current_structure.lattice, to_unit_cell=False,
coords_are_cartesian=False,
properties=site.properties)
self.add_site(site_image)
coords = site_image.coords
vis_radius = tag_style['radius']
color = tag_style['color']
opacity = tag_style['opacity']
self.add_partial_sphere(coords=coords, radius=vis_radius,
color=color, start=0, end=360,
opacity=opacity)
def set_animated_movie_options(self, animated_movie_options=None):
if animated_movie_options is None:
self.animated_movie_options = self.DEFAULT_ANIMATED_MOVIE_OPTIONS.copy()
else:
self.animated_movie_options = self.DEFAULT_ANIMATED_MOVIE_OPTIONS.copy()
for key in animated_movie_options:
if key not in self.DEFAULT_ANIMATED_MOVIE_OPTIONS.keys():
raise ValueError('Wrong option for animated movie')
self.animated_movie_options.update(animated_movie_options)
def display_help(self):
"""
Display the help for various keyboard shortcuts.
"""
helptxt = ["h : Toggle help",
"A/a, B/b or C/c : Increase/decrease cell by one a,"
" b or c unit vector", "# : Toggle showing of polyhedrons",
"-: Toggle showing of bonds", "r : Reset camera direction",
"[/]: Decrease or increase poly_radii_tol_factor "
"by 0.05. Value = " + str(self.poly_radii_tol_factor),
"Up/Down: Rotate view along Up direction by 90 "
"clockwise/anticlockwise",
"Left/right: Rotate view along camera direction by "
"90 clockwise/anticlockwise", "s: Save view to image.png",
"o: Orthogonalize structure",
"n: Move to next structure",
"p: Move to previous structure",
"m: Animated movie of the structures"]
self.helptxt_mapper.SetInput("\n".join(helptxt))
self.helptxt_actor.SetPosition(10, 10)
self.helptxt_actor.VisibilityOn()
def display_warning(self, warning):
self.warningtxt_mapper = vtk.vtkTextMapper()
tprops = self.warningtxt_mapper.GetTextProperty()
tprops.SetFontSize(14)
tprops.SetFontFamilyToTimes()
tprops.SetColor(1, 0, 0)
tprops.BoldOn()
tprops.SetJustificationToRight()
self.warningtxt = "WARNING : {}".format(warning)
self.warningtxt_actor = vtk.vtkActor2D()
self.warningtxt_actor.VisibilityOn()
self.warningtxt_actor.SetMapper(self.warningtxt_mapper)
self.ren.AddActor(self.warningtxt_actor)
self.warningtxt_mapper.SetInput(self.warningtxt)
winsize = self.ren_win.GetSize()
self.warningtxt_actor.SetPosition(winsize[0]-10, 10)
self.warningtxt_actor.VisibilityOn()
def erase_warning(self):
self.warningtxt_actor.VisibilityOff()
def display_info(self, info):
self.infotxt_mapper = vtk.vtkTextMapper()
tprops = self.infotxt_mapper.GetTextProperty()
tprops.SetFontSize(14)
tprops.SetFontFamilyToTimes()
tprops.SetColor(0, 0, 1)
tprops.BoldOn()
tprops.SetVerticalJustificationToTop()
self.infotxt = "INFO : {}".format(info)
self.infotxt_actor = vtk.vtkActor2D()
self.infotxt_actor.VisibilityOn()
self.infotxt_actor.SetMapper(self.infotxt_mapper)
self.ren.AddActor(self.infotxt_actor)
self.infotxt_mapper.SetInput(self.infotxt)
winsize = self.ren_win.GetSize()
self.infotxt_actor.SetPosition(10, winsize[1]-10)
self.infotxt_actor.VisibilityOn()
def erase_info(self):
self.infotxt_actor.VisibilityOff()
class MultiStructuresInteractorStyle(StructureInteractorStyle):
def __init__(self, parent):
StructureInteractorStyle.__init__(self, parent=parent)
def keyPressEvent(self, obj, event):
parent = obj.GetCurrentRenderer().parent
sym = parent.iren.GetKeySym()
if sym == "n":
if parent.istruct == len(parent.structures) - 1:
parent.display_warning('LAST STRUCTURE')
parent.ren_win.Render()
else:
parent.istruct += 1
parent.current_structure = parent.structures[parent.istruct]
parent.set_structure(parent.current_structure, reset_camera=False, to_unit_cell=False)
parent.erase_warning()
parent.ren_win.Render()
elif sym == "p":
if parent.istruct == 0:
parent.display_warning('FIRST STRUCTURE')
parent.ren_win.Render()
else:
parent.istruct -= 1
parent.current_structure = parent.structures[parent.istruct]
parent.set_structure(parent.current_structure, reset_camera=False, to_unit_cell=False)
parent.erase_warning()
parent.ren_win.Render()
elif sym == "m":
parent.istruct = 0
parent.current_structure = parent.structures[parent.istruct]
parent.set_structure(parent.current_structure, reset_camera=False, to_unit_cell=False)
parent.erase_warning()
parent.ren_win.Render()
nloops = parent.animated_movie_options['number_of_loops']
tstep = parent.animated_movie_options['time_between_frames']
tloops = parent.animated_movie_options['time_between_loops']
if parent.animated_movie_options['looping_type'] == 'restart':
loop_istructs = range(len(parent.structures))
elif parent.animated_movie_options['looping_type'] == 'palindrome':
loop_istructs = range(len(parent.structures))+range(len(parent.structures)-2, -1, -1)
else:
raise ValueError('"looping_type" should be "restart" or "palindrome"')
for iloop in range(nloops):
for istruct in loop_istructs:
time.sleep(tstep)
parent.istruct = istruct
parent.current_structure = parent.structures[parent.istruct]
parent.set_structure(parent.current_structure, reset_camera=False, to_unit_cell=False)
parent.display_info('Animated movie : structure {:d}/{:d} '
'(loop {:d}/{:d})'.format(istruct+1, len(parent.structures),
iloop+1, nloops))
parent.ren_win.Render()
time.sleep(tloops)
parent.erase_info()
parent.display_info('Ended animated movie ...')
parent.ren_win.Render()
StructureInteractorStyle.keyPressEvent(self, obj, event)
|
matk86/pymatgen
|
pymatgen/vis/structure_vtk.py
|
Python
|
mit
| 47,013
|
[
"Jmol",
"VTK",
"pymatgen"
] |
59014ea6d82d56f216371e645f45833f720d6b366f2e1240c3a3c271fae3ea81
|
#!BPY
"""
Name: 'Sunflow Exporter (.sc)...'
Blender: 2.4
Group: 'Export'
Tip: ''
"""
"""
Version : 0.07.0 (January 2007)
Author : R Lindsay (hayfever) / Christopher Kulla
Description : Export to Sunflow renderer http://sunflow.sourceforge.net/
"""
## imports ##
import Blender, os, sys, time, struct
from Blender import Mathutils, NMesh, Lamp, Object, Scene, Mesh, Material, Draw, BGL
from math import *
## end imports ##
## global gui vars ##
MINAA = Draw.Create(-2)
MAXAA = Draw.Create(0)
AASAMPLES = Draw.Create(1)
DSAMPLES = Draw.Create(16)
IMGFILTER = Draw.Create(1)
IMGFILTERW = Draw.Create(1)
IMGFILTERH = Draw.Create(1)
DOF = Draw.Create(0)
DOFRADIUS = Draw.Create(1.0)
DOFDIST = Draw.Create(10.0)
SPHERICALCAMERA = Draw.Create(0)
MESHLIGHTPOWER = Draw.Create(1)
OCCLUSSION = Draw.Create(0)
OCCBRIGHTR = Draw.Create(1.0)
OCCBRIGHTG = Draw.Create(1.0)
OCCBRIGHTB = Draw.Create(1.0)
OCCDARKR = Draw.Create(0.0)
OCCDARKG = Draw.Create(0.0)
OCCDARKB = Draw.Create(0.0)
OCCSAMPLES = Draw.Create(32)
OCCDIST = Draw.Create(0.0)
EXPORT_EVT = 1
NO_EVENT = 2
DOF_CAMERA = 3
SPHER_CAMERA = 4
IRR_EVENT = 5
FILTER_EVENT = 7
CHANGE_AA = 8
CHANGE_CAM = 10
CHANGE_ACC = 11
CHANGE_LIGHT = 12
CHANGE_AO = 13
## export options
EXP_ANIM = Draw.Create(0)
IMGFILTERLIST = ["box", "gaussian", "mitchell", "triangle", "catmull-rom", "blackman-harris", "sinc", "lanczos"]
## end global gui vars ##
## global vars ##
FILENAME = Blender.Get('filename').replace(".blend", ".sc")
global FILE
global SCENE
global IM_HEIGHT
global IM_WIDTH
global TEXTURES
global OBJECTS
global IBLLIGHT
global LAYERS
global SCREEN
## end global vars ##
## start of export ##
print "\n\n"
print "blend2sunflow v0.07.0"
## Export logic for simple options
def export_output():
print "o exporting output details..."
FILE.write("image {\n")
FILE.write("\tresolution %d %d\n" % (IM_WIDTH, IM_HEIGHT))
FILE.write("\taa %s %s\n" % (MINAA.val, MAXAA.val))
FILE.write("\tfilter %s\n" % IMGFILTERLIST[IMGFILTER.val-1])
FILE.write("}")
FILE.write("\n")
## Export logic for materials
def export_shaders():
print "o exporting shaders..."
# default shader
FILE.write("\n\nshader {\n\tname def\n\ttype diffuse\n\tdiff 1 1 1\n}")
if OCCLUSSION.val == 1:
FILE.write("\n\nshader {\n name amboccshader\n type amb-occ2\n")
FILE.write("\tbright { \"sRGB nonlinear\" %s %s %s }\n" % (OCCBRIGHTR.val, OCCBRIGHTG.val, OCCBRIGHTB.val))
FILE.write("\tdark { \"sRGB nonlinear\" %s %s %s }\n" % (OCCDARKR.val, OCCDARKG.val, OCCDARKB.val))
FILE.write("\tsamples %s\n" % OCCSAMPLES.val)
FILE.write("\tdist %s\n}" % OCCDIST.val)
FILE.write("\n\noverride amboccshader true")
materials = Blender.Material.get()
for mat in materials:
FILE.write("\n\nshader {\n")
FILE.write("\tname \""+mat.name+".shader\"\n")
textures = mat.getTextures()
flags = mat.getMode()
if textures[0] <> None and textures[0].tex.getType() == "Image":
textu = textures[0]
if mat.name.startswith("sfambocc"):
print " o exporting ambient occlusion texture shader "+mat.name+"..."
FILE.write("\ttype amb-occ\n")
else:
print " o exporting diffuse texture shader "+mat.name+"..."
FILE.write("\ttype diffuse\n")
FILE.write("\ttexture \"" + textu.tex.getImage().getFilename() + "\"\n}")
else:
RGB = mat.getRGBCol()
## shiny shader
if mat.name.startswith("sfshiny"):
print " o exporting shiny shader "+mat.name+"..."
FILE.write("\ttype shiny\n")
FILE.write("\tdiff { \"sRGB nonlinear\" %s %s %s }\n" % (RGB[0], RGB[1], RGB[2]))
FILE.write("\trefl %s\n}" % mat.getRayMirr())
## amb-occ shader
elif mat.name.startswith("sfambocc"):
print " o exporting ambient occlusion shader "+mat.name+"..."
FILE.write("\ttype amb-occ\n")
FILE.write("\tdiff { \"sRGB nonlinear\" %s %s %s }\n}" % (RGB[0], RGB[1], RGB[2]))
## phong shader
elif mat.name.startswith("sfphong"):
print " o exporting phong shader "+ mat.name+"..."
FILE.write("\ttype phong\n")
FILE.write("\tdiff { \"sRGB nonlinear\" %s %s %s }\n" % (RGB[0],RGB[1],RGB[2]))
speccol = mat.specCol
FILE.write("\tspec { \"sRGB nonlinear\" %s %s %s } %s\n" %(speccol[0], speccol[1], speccol[2], mat.hard))
FILE.write("\tsamples 4\n}")
## reflection shader
elif flags & Material.Modes['RAYMIRROR']:
print " o exporting mirror shader "+mat.name+"..."
FILE.write("\ttype mirror\n")
FILE.write("\trefl { \"sRGB nonlinear\" %s %s %s }\n}" %(RGB[0],RGB[1],RGB[2]))
## glass shader
elif flags & Material.Modes['RAYTRANSP']:
print " o exporting glass shader "+mat.name+"..."
FILE.write("\ttype glass\n")
FILE.write("\teta " + str(mat.getIOR()) + "\n")
FILE.write("\tcolor { \"sRGB nonlinear\" %s %s %s }\n}" %(RGB[0],RGB[1],RGB[2]))
## diffuse shader
else:
print " o exporting diffuse shader "+mat.name+"..."
FILE.write("\ttype diffuse\n")
FILE.write("\tdiff { \"sRGB nonlinear\" %s %s %s }\n}" %(RGB[0],RGB[1],RGB[2]))
## Export logic for Blender's light sources
def export_lights(lmp):
# only lamp type 0 supported at the moment
# lamp types are: 0 - Lamp, 1 - Sun, 2 - Spot, 3 - Hemi, 4 - Area
lamp = lmp.getData()
if lamp.type == 0:
print "o exporting lamp "+lmp.name+"..."
# get the rgb component for the lamp
red = lamp.col[0]
green = lamp.col[1]
blue = lamp.col[2]
power = lamp.energy
# get the location of the lamp
objmatrix = lmp.matrix
lampV = Mathutils.Vector([0, 0, 0, 1])
lampV = lampV * objmatrix
FILE.write("\n\nlight {\n")
FILE.write("\ttype point\n")
FILE.write("\tcolor { \"sRGB nonlinear\" %s %s %s }\n" % (red, green, blue))
FILE.write("\tpower %s\n" % (power))
FILE.write("\tp %s %s %s\n" % (lampV[0], lampV[1], lampV[2]))
FILE.write("}")
elif lamp.type == 1:
print "o exporting sun-light "+lmp.name+"..."
invmatrix = Mathutils.Matrix(lmp.getInverseMatrix())
FILE.write("\nlight {\n")
FILE.write("\ttype sunsky\n")
FILE.write("\tup 0 0 1\n")
FILE.write("\teast 0 1 0\n")
FILE.write("\tsundir %f %f %f\n" % (invmatrix[0][2], invmatrix[1][2], invmatrix[2][2]))
FILE.write("\tturbidity 6\n")
FILE.write("\tsamples %s\n" % DSAMPLES.val)
FILE.write("}")
elif lamp.type == 4:
print "o exporting area-light "+lmp.name+"..."
objmatrix = lmp.matrix
size = lamp.areaSizeX * 0.5
lampV0 = Mathutils.Vector([-size, size, 0, 1])
lampV1 = Mathutils.Vector([ size, size, 0, 1])
lampV2 = Mathutils.Vector([ size, -size, 0, 1])
lampV3 = Mathutils.Vector([-size, -size, 0, 1])
lampV0 = lampV0 * objmatrix
lampV1 = lampV1 * objmatrix
lampV2 = lampV2 * objmatrix
lampV3 = lampV3 * objmatrix
red = lamp.col[0]
green = lamp.col[1]
blue = lamp.col[2]
radiance = lamp.energy * MESHLIGHTPOWER.val
FILE.write("\n\nlight {\n")
FILE.write("\ttype meshlight\n")
FILE.write("\tname \"%s\"\n" % (lmp.name))
FILE.write("\temit { \"sRGB nonlinear\" %s %s %s }\n" % (red, green, blue))
FILE.write("\tradiance %s\n" % (radiance))
FILE.write("\tsamples %s\n" % DSAMPLES.val)
FILE.write("\tpoints 4\n")
FILE.write("\t\t%s %s %s\n" % (lampV0[0], lampV0[1], lampV0[2]))
FILE.write("\t\t%s %s %s\n" % (lampV1[0], lampV1[1], lampV1[2]))
FILE.write("\t\t%s %s %s\n" % (lampV2[0], lampV2[1], lampV2[2]))
FILE.write("\t\t%s %s %s\n" % (lampV3[0], lampV3[1], lampV3[2]))
FILE.write("\ttriangles 2\n")
FILE.write("\t\t0 1 2\n")
FILE.write("\t\t0 2 3\n")
FILE.write("}")
#elif lamp.type == 2:
# print "o exporting spotlight "+lmp.name+"..."
# FILE.write("\n\nlight {\n")
# FILE.write("\ttype directional\n")
# FILE.write("\ttarget\n")
# FILE.write("\tradius %s\n" % lamp.getSpotSize())
# FILE.write("\temit %s %s %s" %(lamp.col[0],lamp.col[1],lamp.col[2])+"\n")
# FILE.write("}")
## Export method for Blender camera
def export_camera(cam):
global IBLLIGHT
# get the camera
camera = cam.getData()
print "o exporting Camera "+camera.getName()+"..."
# get the object matrix so we can calculate to and up
objmatrix = cam.matrix
eyeV = Mathutils.Vector([0, 0, 0, 1])
targetV = Mathutils.Vector([0, 0, -1, 1])
upV = Mathutils.Vector([0, 1, 0, 0])
eyeV = eyeV * objmatrix
targetV = targetV * objmatrix
upV = upV * objmatrix
# get the fov value
fov = 360.0 * atan(16.0 / camera.getLens()) / pi
FILE.write("\n\ncamera {\n")
camtype = "pinhole"
if(DOF.val == 1): camtype = "thinlens"
if(SPHERICALCAMERA.val == 1): camtype = "spherical"
FILE.write("\ttype %s\n" % camtype)
FILE.write("\teye %s %s %s\n" % (eyeV[0], eyeV[1], eyeV[2]))
FILE.write("\ttarget %s %s %s\n" % (targetV[0], targetV[1], targetV[2]))
FILE.write("\tup %s %s %s\n" % (upV[0], upV[1], upV[2]))
if SPHERICALCAMERA.val == 0: FILE.write("\tfov %s \n" % fov)
if SPHERICALCAMERA.val == 0: FILE.write("\taspect %s \n" % (1.0 * IM_WIDTH / IM_HEIGHT))
if DOF.val == 1:
FILE.write("\tfdist %s \n" % DOFDIST)
FILE.write("\tlensr %s \n" % DOFRADIUS)
FILE.write("}")
if IBLLIGHT <> "":
print "o exporting ibllight..."
FILE.write("\n\nlight {\n")
FILE.write("\ttype ibl\n")
FILE.write("\timage \"%s\"\n" % (IBLLIGHT))
FILE.write("\tcenter 1 0 0\n")
FILE.write("\tup 0 0 1\n")
FILE.write("\tlock true\n")
FILE.write("\tsamples %s\n" % DSAMPLES.val)
FILE.write("}")
## Export method for meshes
def export_geometry(obj, filename):
#mesh = "";verts="";faces="";numverts=""
islight = obj.name.startswith("meshlight")
if islight:
print "o exporting meshlight " + obj.name+"..."
else:
print "o exporting mesh " + obj.name+"..."
# get the mesh data
mesh = NMesh.GetRawFromObject(obj.name)
if islight:
mesh.transform(obj.getMatrix(), 1)
verts = mesh.verts
faces = mesh.faces
numfaces = faces.__len__()
numverts = verts.__len__()
if numfaces > 100000:
print " -> large mesh detected - creating binary ra3 file"
ra3filename = filename.replace(".sc", "_%s.ra3" % obj.name)
RA3FILE = open(ra3filename, 'wb')
print " -> creating \"%s\" ..." % ra3filename
print " -> counting triangles ..."
numtris = 0
for face in faces:
num = len(face.v)
if num == 4:
numtris = numtris + 2
elif num == 3:
numtris = numtris + 1
print " -> writing %s points" % numverts
RA3FILE.write(struct.pack("<II", numverts, numtris))
for vert in verts:
RA3FILE.write(struct.pack("<fff", vert.co[0], vert.co[1], vert.co[2]))
print " -> writing %s triangles" % numtris
for face in faces:
num = len(face.v)
if num == 4:
RA3FILE.write(struct.pack("<III", face.v[0].index, face.v[1].index, face.v[2].index))
RA3FILE.write(struct.pack("<III", face.v[0].index, face.v[2].index, face.v[3].index))
elif num == 3:
RA3FILE.write(struct.pack("<III", face.v[0].index, face.v[1].index, face.v[2].index))
RA3FILE.close()
print " -> done writing file"
FILE.write("\n\nobject {\n")
if len(mesh.materials) == 1:
FILE.write("\tshader \"" + mesh.materials[0].name + ".shader\"\n")
elif len(mesh.materials) > 1:
FILE.write("\tshaders %d\n" % (len(mesh.materials)))
for mat in mesh.materials:
FILE.write("\t\t\"" + mat.name + ".shader\"\n")
else:
FILE.write("\tshader def\n")
mat = obj.getMatrix()
FILE.write("\ttransform col\n\t\t%s %s %s %s\n\t\t%s %s %s %s\n\t\t%s %s %s %s\n\t\t%s %s %s %s\n" % (
mat[0][0], mat[0][1], mat[0][2], mat[0][3],
mat[1][0], mat[1][1], mat[1][2], mat[1][3],
mat[2][0], mat[2][1], mat[2][2], mat[2][3],
mat[3][0], mat[3][1], mat[3][2], mat[3][3]))
FILE.write("\ttype file-mesh\n")
FILE.write("\tname \"" + obj.name + "\"\n")
FILE.write("\tfilename \"%s\"\n" % os.path.basename(ra3filename))
FILE.write("}\n")
return
if numverts > 0:
if islight:
FILE.write("\n\nlight {\n")
FILE.write("\ttype meshlight\n")
FILE.write("\tname \"" + obj.name + "\"\n")
if len(mesh.materials) >= 1:
matrl = mesh.materials[0]
FILE.write("\temit { \"sRGB nonlinear\" %s %s %s }\n" % (matrl.R, matrl.G, matrl.B))
else:
FILE.write("\temit 1 1 1\n")
FILE.write("\tradiance %s\n" % (MESHLIGHTPOWER.val))
FILE.write("\tsamples %s\n" % DSAMPLES.val)
else:
FILE.write("\n\nobject {\n")
if len(mesh.materials) == 1:
FILE.write("\tshader \"" + mesh.materials[0].name + ".shader\"\n")
elif len(mesh.materials) > 1:
FILE.write("\tshaders %d\n" % (len(mesh.materials)))
for mat in mesh.materials:
FILE.write("\t\t\"" + mat.name + ".shader\"\n")
else:
FILE.write("\tshader def\n")
mat = obj.getMatrix()
FILE.write("\ttransform col\n\t\t%s %s %s %s\n\t\t%s %s %s %s\n\t\t%s %s %s %s\n\t\t%s %s %s %s\n" % (
mat[0][0], mat[0][1], mat[0][2], mat[0][3],
mat[1][0], mat[1][1], mat[1][2], mat[1][3],
mat[2][0], mat[2][1], mat[2][2], mat[2][3],
mat[3][0], mat[3][1], mat[3][2], mat[3][3]))
FILE.write("\ttype generic-mesh\n")
FILE.write("\tname \"" + obj.name + "\"\n")
FILE.write("\tpoints %d\n" % (numverts))
for vert in verts:
FILE.write("\t\t%s %s %s\n" % (vert.co[0], vert.co[1], vert.co[2]))
numtris = 0
for face in faces:
num = len(face.v)
if num == 4:
numtris = numtris + 2
elif num == 3:
numtris = numtris + 1
FILE.write("\ttriangles %d\n" % (numtris))
allsmooth = True
allflat = True
for face in faces:
num = len(face.v)
smooth = face.smooth != 0
allsmooth &= smooth
allflat &= not smooth
if num == 4:
FILE.write("\t\t%d %d %d\n" % (face.v[0].index, face.v[1].index, face.v[2].index))
FILE.write("\t\t%d %d %d\n" % (face.v[0].index, face.v[2].index, face.v[3].index))
elif num == 3:
FILE.write("\t\t%d %d %d\n" % (face.v[0].index, face.v[1].index, face.v[2].index))
## what kind of normals do we have?
if not islight:
if allflat:
FILE.write("\tnormals none\n")
elif allsmooth:
FILE.write("\tnormals vertex\n")
for vert in verts:
FILE.write("\t\t%s %s %s\n" % (vert.no[0], vert.no[1], vert.no[2]))
else:
FILE.write("\tnormals facevarying\n")
for face in faces:
num = len(face.v)
if face.smooth != 0:
if num == 4:
index0 = face.v[0].index
index1 = face.v[1].index
index2 = face.v[2].index
index3 = face.v[3].index
FILE.write("\t\t%s %s %s %s %s %s %s %s %s\n" % (verts[index0].no[0], verts[index0].no[1], verts[index0].no[2],
verts[index1].no[0], verts[index1].no[1], verts[index1].no[2],
verts[index2].no[0], verts[index2].no[1], verts[index2].no[2]))
FILE.write("\t\t%s %s %s %s %s %s %s %s %s\n" % (verts[index0].no[0], verts[index0].no[1], verts[index0].no[2],
verts[index2].no[0], verts[index2].no[1], verts[index2].no[2],
verts[index3].no[0], verts[index3].no[1], verts[index3].no[2]))
elif num == 3:
index0 = face.v[0].index
index1 = face.v[1].index
index2 = face.v[2].index
FILE.write("\t\t%s %s %s %s %s %s %s %s %s\n" % (verts[index0].no[0], verts[index0].no[1], verts[index0].no[2],
verts[index1].no[0], verts[index1].no[1], verts[index1].no[2],
verts[index2].no[0], verts[index2].no[1], verts[index2].no[2]))
else:
fnx = face.no[0]
fny = face.no[1]
fnz = face.no[2]
if num == 4:
FILE.write("\t\t%s %s %s %s %s %s %s %s %s\n" % (fnx, fny, fnz, fnx, fny, fnz, fnx, fny, fnz))
FILE.write("\t\t%s %s %s %s %s %s %s %s %s\n" % (fnx, fny, fnz, fnx, fny, fnz, fnx, fny, fnz))
elif num == 3:
FILE.write("\t\t%s %s %s %s %s %s %s %s %s\n" % (fnx, fny, fnz, fnx, fny, fnz, fnx, fny, fnz))
if mesh.hasFaceUV():
tx = 1
ty = 1
if len(mesh.materials) >= 1:
if len(mesh.materials[0].getTextures()) >= 1:
if mesh.materials[0].getTextures()[0] <> None:
tx = mesh.materials[0].getTextures()[0].tex.repeat[0]
ty = mesh.materials[0].getTextures()[0].tex.repeat[1]
FILE.write("\tuvs facevarying\n")
for face in faces:
num = len(face.v)
if num == 4:
FILE.write("\t\t%s %s %s %s %s %s\n" % (tx * face.uv[0][0], ty * face.uv[0][1], tx * face.uv[1][0], ty * face.uv[1][1], tx * face.uv[2][0], ty * face.uv[2][1]))
FILE.write("\t\t%s %s %s %s %s %s\n" % (tx * face.uv[0][0], ty * face.uv[0][1], tx * face.uv[2][0], ty * face.uv[2][1], tx * face.uv[3][0], ty * face.uv[3][1]))
elif num == 3:
FILE.write("\t\t%s %s %s %s %s %s\n" % (tx * face.uv[0][0], ty * face.uv[0][1], tx * face.uv[1][0], ty * face.uv[1][1], tx * face.uv[2][0], ty * face.uv[2][1]))
else:
FILE.write("\tuvs none\n")
if len(mesh.materials) > 1:
FILE.write("\tface_shaders\n")
for face in faces:
num = len(face.v)
if num == 4:
FILE.write("\t\t%d\n" % (face.materialIndex))
FILE.write("\t\t%d\n" % (face.materialIndex))
elif num == 3:
FILE.write("\t\t%d\n" % (face.materialIndex))
FILE.write("}\n")
## Main export method
def exportfile(filename):
global FILE, SCENE, IM_HEIGHT, IM_WIDTH, TEXTURES, OBJECTS, LAYERS, IBLLIGHT, EXP_ANIM
SCENE = Blender.Scene.GetCurrent()
IM_HEIGHT = SCENE.getRenderingContext().imageSizeY()
IM_WIDTH = SCENE.getRenderingContext().imageSizeX()
TEXTURES = Blender.Texture.Get()
LAYERS = SCENE.getLayers()
STARTFRAME = SCENE.getRenderingContext().startFrame()
ENDFRAME = SCENE.getRenderingContext().endFrame()
CTX = SCENE.getRenderingContext()
orig_frame = CTX.currentFrame()
if not filename.endswith(".sc"):
filename = filename + ".sc"
fname = filename
ANIM = EXP_ANIM.val
if ANIM == 1:
base = os.path.splitext(os.path.basename(filename))[0]
FILE = open(filename.replace(".sc", ".java"), "wb")
FILE.write("""
public void build() {
parse("%s" + ".settings.sc");
parse("%s" + "." + getCurrentFrame() + ".sc");
}
""" % (base, base))
FILE.close()
FILE = open(filename.replace(".sc", ".settings.sc"), "wb")
export_output()
FILE.close()
else:
STARTFRAME = ENDFRAME = orig_frame
for cntr in range(STARTFRAME, ENDFRAME + 1):
filename = fname
CTX.currentFrame(cntr)
SCENE.makeCurrent()
try:
ibllighttext = Blender.Texture.Get("ibllight")
if ibllighttext <> "":
if ibllighttext <> None and ibllighttext.getType() == "Image":
IBLLIGHT = ibllighttext.getImage().getFilename()
except:
IBLLIGHT = ""
OBJECTS = Blender.Scene.GetCurrent().getChildren()
if ANIM == 1:
filename = filename.replace(".sc", ".%d.sc" % (CTX.currentFrame()))
print "Exporting to: %s" % (filename)
FILE = open(filename, 'wb')
if ANIM == 0:
export_output()
export_shaders()
export_camera(SCENE.getCurrentCamera())
for object in OBJECTS:
if object.users > 1 and object.layers[0] in LAYERS:
if object.getType() == 'Lamp':
export_lights(object)
if object.getType() == 'Mesh' or object.getType() == 'Surf':
if object.name.startswith("meshlight"):
export_geometry(object, filename)
if ANIM == 0:
FILE.write("\n\ninclude \"%s\"\n" % (os.path.basename(filename).replace(".sc", ".geo.sc")))
FILE.close()
## open geo file
filename = filename.replace(".sc", ".geo.sc")
print "Exporting geometry to: %s" % (filename)
FILE = open(filename, 'wb')
for object in OBJECTS:
if object.users > 1 and object.layers[0] in LAYERS:
if object.getType() == 'Mesh' or object.getType() == 'Surf':
if not object.name.startswith("meshlight"):
export_geometry(object, filename)
FILE.close()
if ANIM == 1:
CTX.currentFrame(orig_frame)
SCENE.makeCurrent()
print "Export finished."
## Global event handler
def event(evt, val):
if evt == Draw.ESCKEY:
print "quitting exporter..."
Draw.Exit()
## GUI button event handler
def buttonEvent(evt):
global FILE,SCREEN
if evt == EXPORT_EVT:
Blender.Window.FileSelector(exportfile, "Export .sc", FILENAME)
if evt == DOF_CAMERA:
if DOF.val == 1:
if SPHERICALCAMERA.val == 1:
SPHERICALCAMERA.val = 0
Draw.Redraw()
if evt == SPHER_CAMERA:
if SPHERICALCAMERA.val == 1:
if DOF.val == 1:
DOF.val = 0
Draw.Redraw()
if evt == IRR_EVENT:
if GIIRR.val == 1:
if GIPATH.val == 1:
GIPATH.val = 0
Draw.Redraw()
if evt == FILTER_EVENT:
Draw.Redraw()
if evt == CHANGE_AA:
SCREEN=0
Draw.Redraw()
return
if evt == CHANGE_CAM:
SCREEN=2
Draw.Redraw()
return
if evt == CHANGE_LIGHT:
SCREEN=4
Draw.Redraw()
return
if evt == CHANGE_AO:
SCREEN=5
Draw.Redraw()
return
## Draws the individual panels
def drawGUI():
global SCREEN
if SCREEN==0:
drawAA()
if SCREEN==2:
drawCamera()
if SCREEN==4:
drawLights()
if SCREEN==5:
drawAO()
## Draw AA settings
def drawAA():
global MINAA, MAXAA, AASAMPLES
global IMGFILTERW, IMGFILTERH, IMGFILTER
global EXP_ANIM
## aa settings
col=10; line=200; BGL.glRasterPos2i(col, line); Draw.Text("AA:")
col=100; MINAA=Draw.Number("Min AA ", 2, col, line, 120, 18, MINAA.val, -4, 5);
col=230; MAXAA=Draw.Number("Max AA ", 2, col, line, 120, 18, MAXAA.val, -4, 5)
col=360; AASAMPLES=Draw.Number("Samples", 2, col, line, 120, 18, AASAMPLES.val, 0, 32)
col=10; line=175; BGL.glRasterPos2i(col, line); Draw.Text("Image Filter:")
col=100; line=173; IMGFILTER=Draw.Menu("%tImage Filter|box|gaussian|mitchell|triangle|catmull-rom|blackman-harris|sinc|lanczos", FILTER_EVENT, col, line, 120, 18, IMGFILTER.val)
col=10; line=120; EXP_ANIM=Draw.Toggle("Export As Animation", 2, col, line, 140, 18, EXP_ANIM.val)
drawButtons()
## Draw camera options
def drawCamera():
global DOF, DOFRADIUS, DOFDIST, SPHERICALCAMERA
## camera settings
col=10; line=200; BGL.glRasterPos2i(col, line); Draw.Text("Camera:")
col=100; line=195; DOF=Draw.Toggle("DOF", DOF_CAMERA, col, line, 120, 18, DOF.val)
col=225; DOFDIST=Draw.Number("Distance", 2, col, line, 120, 18, DOFDIST.val, 0.0, 200.00)
col=350; DOFRADIUS=Draw.Number("Radius", 2, col, line, 120, 18, DOFRADIUS.val, 0.0, 200.00)
col=100; line=170; SPHERICALCAMERA=Draw.Toggle("Spherical", SPHER_CAMERA, col, line, 120, 18, SPHERICALCAMERA.val)
drawButtons()
## Draw light options
def drawLights():
global MESHLIGHTPOWER, DSAMPLES
## meshlight power slider
col=10; line=200; BGL.glRasterPos2i(col, line); Draw.Text("Meshlight:")
col=100; line=195; MESHLIGHTPOWER=Draw.Number("Power", 2, col, line, 120, 18, MESHLIGHTPOWER.val, 1, 15)
## lightserver settings
col=10; line=150; BGL.glRasterPos2i(col, line); Draw.Text("Lightserver:")
col=100; line=147; DSAMPLES=Draw.Number("Direct Samples ", 2, col, line, 250, 18, DSAMPLES.val, 0, 1024);
drawButtons()
## Draw ambient occlusion override settings
def drawAO():
global OCCLUSSION, OCCBRIGHTR, OCCBRIGHTG, OCCBRIGHTB, OCCDARKR, OCCDARKG, OCCDARKB, OCCSAMPLES, OCCDIST
col=10; line=200; BGL.glRasterPos2i(col, line); Draw.Text("Ambient Occlusion")
col=10; line=175; OCCLUSSION=Draw.Toggle("Amb Occ", 2, col, line, 85, 18, OCCLUSSION.val)
col=100; OCCBRIGHTR=Draw.Number("Bright (R)", 2, col, line, 125, 18, OCCBRIGHTR.val, 0.0, 1.0)
col=230; OCCBRIGHTG=Draw.Number("Bright (G)", 2, col, line, 125, 18, OCCBRIGHTG.val, 0.0, 1.0)
col=360; OCCBRIGHTB=Draw.Number("Bright (B)", 2, col, line, 125, 18, OCCBRIGHTB.val, 0.0, 1.0)
col=100; line=150; OCCDARKR=Draw.Number("Dark (R)", 2, col, line, 125, 18, OCCDARKR.val, 0.00, 1.0)
col=230; OCCDARKG=Draw.Number("Dark (G)", 2, col, line, 125, 18, OCCDARKG.val, 0.0, 1.0)
col=360; OCCDARKB=Draw.Number("Dark (B)", 2, col, line, 125, 18, OCCDARKB.val, 0.0, 1.0)
col=100; line=125; OCCSAMPLES=Draw.Number("Samples", 2, col, line, 125, 18, OCCSAMPLES.val, 0, 256)
col=230; OCCDIST=Draw.Number("Distance", 2, col, line, 125, 18, OCCDIST.val, -1.0, 150.0)
drawButtons()
## Draw the bottom bar of buttons in the interface
def drawButtons():
Draw.Button("Export" , EXPORT_EVT , 20 , 10, 90, 20)
Draw.Button("AA" , CHANGE_AA , 20 , 40, 90, 20)
Draw.Button("Camera" , CHANGE_CAM , 115, 40, 90, 20)
Draw.Button("Light" , CHANGE_LIGHT, 210, 40, 90, 20)
Draw.Button("AO Override", CHANGE_AO , 305, 40, 90, 20)
SCREEN=0
Draw.Register(drawGUI, event, buttonEvent)
|
Acbentle/terrain474
|
exporters/blender/sunflow_export.py
|
Python
|
mit
| 32,579
|
[
"Gaussian"
] |
c69c3f15c374e80d65e5d4ef815e7cfa317f98c1f4498d1d6abc67475704713e
|
# python script, to extract circular reads from a bam file, based on a tab-separated circle_id - reads file and a bam file. writes out circle-specific bam files
# input: tab-separated file with circle id as chr:start-end\tlist with read names
# input: bamfile containing circle reads (as well as others)
# output: circle specific bam files, folder for each sample
import os
import pysam
import argparse
parser = argparse.ArgumentParser(description='Extracts circular reads based on circle_file from the sample.bam and writes them into circle separated bamfiles.')
# input
parser.add_argument('circlefile', metavar = 'sample_circleIDs.txt', help = 'tab separated file chr:start_end(tab)read1,read2,read3.' )
parser.add_argument('bamfile', metavar = 'sample.bam', help = 'bamfile containing chimeric reads, linear reads may be in it but are not required.')
# output
parser.add_argument('outputfolder', metavar = 'folder', help = 'outfolder, there will be a subfolder for the sample containing a bam file for each circle.')
parser.add_argument('sample', metavar = 'sample_name', help = 'sample_name to title every thing.')
# options
parser.add_argument('-r', dest = 'reads', default = 5, type = int, help = 'Circle has to have at least <r> reads to be analysed.')
parser.add_argument('-q', dest = 'mapq', default = 3, type = int, help = 'MAPQ cutoff, only reads passing this threshold will be written to circle bamfile.')
parser.add_argument('--tmp', dest = 'tmp_folder', default = '.', help = 'tempfolder to store tempfiles generated by pybedtools.')
args = parser.parse_args()
# parse arguments
circles = args.circlefile
bamfile = args.bamfile
outfolder = args.outputfolder
sample = args.sample
cutoff = args.reads
mapq_cutoff = args.mapq
tmp_folder = args.tmp_folder
# include some checks to make sure input was provided correctly
# define functions
def read_circles(infile):
'''
for each circle, extracts all reads_ids, but also accumulates all circular reads ids independent of circle id.
'''
circle_IDs = {}
reads = {}
I = open(infile)
for circle in I:
if not circle.startswith('#'):
circle_IDs[circle.split('\t')[0]] = circle.replace('\n', '').split('\t')[1].split(',') [:-1]
for lola in circle.replace('\n', '').split('\t')[1].split(',') [:-1]:
reads[lola] = 0
I.close()
return(circle_IDs, reads)
def load_alignment(infile, circle_reads, cutoff):
'''
loads sample bamfile and extracts all circular reads based on read list obtained from read_circles or any given list of read ids.
'''
reads = {}
if 'bam' in infile.split('.')[-1] :
samfile = pysam.AlignmentFile(bamfile, 'rb')
else:
samfile = pysam.AlignmentFile(bamfile, 'r')
for i,read in enumerate(samfile.fetch()):
if i % 1000000 == 0:
print('%s reads processed' %(i))
if read.qname in circle_reads and read.mapq > cutoff:
#print(float(i)/17000000)
if not read.qname in reads:
reads[read.qname] = {}
reads[read.qname][i] = read
samfile.close()
return(reads)
def write_circle_bam(reads, circles, cutoff, template, outfolder):
'''
for each circle, writes a bam file containing only reads spanning the circle junction and their mates if mates are present.
'''
samfile = pysam.AlignmentFile(template, 'rb')
for circle in circles:
if len(circles[circle]) >= cutoff:
circle_bam = pysam.AlignmentFile("%s/%s_%sreads.bam" %(outfolder, circle.replace(':', '_').replace('|', '_'), len(circles[circle])), "wb", template=samfile)
for read in circles[circle]:
if read in reads:
for part in reads[read]:
circle_bam.write(reads[read][part])
circle_bam.close()
samfile.close()
return
# run script
circle_info, circle_reads = read_circles(circles)
print('DONE reading circles, found %s circles' %(len(circle_info)))
reads = load_alignment(bamfile, circle_reads, mapq_cutoff)
print('DONE extracting circular reads')
folders = os.listdir(outfolder)
if not sample in folders:
os.mkdir('%s/%s' %(outfolder, sample))
write_circle_bam(reads, circle_info, cutoff, bamfile, '%s/%s' %(outfolder, sample))
print('DONE writing circle bam files\n')
files = os.listdir('%s/%s' %(outfolder, sample))
print('%s circles passed your thresholds of at least %s reads with at least a mapq of %s\n\n' %(len(files), cutoff, mapq_cutoff))
for f in files:
if f.split('.')[-1] == 'bam':
pysam.sort('%s/%s/%s' %(outfolder, sample, f), '%s/%s/%s' %(outfolder, sample, f.replace('.bam', '.sorted')))
pysam.index('%s/%s/%s.bam' %(outfolder, sample, f.replace('.bam', '.sorted')))
os.system('rm %s/%s/%s' %(outfolder, sample, f))
|
dieterich-lab/FUCHS
|
GCB_testset/FUCHS/extract_reads.py
|
Python
|
gpl-3.0
| 4,638
|
[
"pysam"
] |
35cb6ce06464c9fec107664d0dba74e304ebbf83b1a76b19e0288cacbba8f3de
|
"""
Test LogLevels module
"""
__RCSID__ = "$Id$"
import logging
import pytest
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
@pytest.mark.parametrize(
"logLevel, value",
[
("debug", logging.DEBUG),
("verbose", 15),
("info", 20),
("warn", logging.WARN),
("notice", 35),
("error", logging.ERROR),
("always", 45),
("fatal", logging.CRITICAL),
("unknown", None),
],
)
def test_getLevelValue(logLevel, value):
"""
Test getLevelValue
"""
assert LogLevels.getLevelValue(logLevel) == value
@pytest.mark.parametrize(
"value, logLevel",
[
(logging.DEBUG, "debug"),
(15, "verbose"),
(20, "info"),
(logging.WARN, "warn"),
(35, "notice"),
(logging.ERROR, "error"),
(45, "always"),
(logging.CRITICAL, "fatal"),
(-1, None),
("error", None),
],
)
def test_getLevel(value, logLevel):
"""
Test getLevel
"""
if logLevel:
logLevel = logLevel.upper()
assert LogLevels.getLevel(value) == logLevel
def test_getLevelNames():
"""
Test getLevelNames
"""
levels = ["DEBUG", "VERBOSE", "INFO", "WARN", "NOTICE", "ERROR", "ALWAYS", "FATAL"]
assert sorted(LogLevels.getLevelNames()) == sorted(levels)
|
ic-hep/DIRAC
|
src/DIRAC/FrameworkSystem/private/standardLogging/test/Test_LogLevels.py
|
Python
|
gpl-3.0
| 1,351
|
[
"DIRAC"
] |
78c417c72683219209aef22dfc07e6640c08678e79c7b0a3315d4a4b1f18e421
|
import vtk
red = [255, 0, 0]
green = [0, 255, 0]
blue = [0, 0, 255]
# Setup the colors array
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
# Add the colors we created to the colors array
colors.InsertNextTypedTuple(red)
colors.InsertNextTypedTuple(red)
colors.InsertNextTypedTuple(blue)
colors.InsertNextTypedTuple(blue)
colors.InsertNextTypedTuple(blue)
colors.InsertNextTypedTuple(green)
colors.InsertNextTypedTuple(green)
colors.InsertNextTypedTuple(green)
colors.InsertNextTypedTuple(red)
colors.InsertNextTypedTuple(blue)
colors.InsertNextTypedTuple(blue)
colors.InsertNextTypedTuple(green)
# Create the geometry of the points (the coordinate)
p0 = [0.0, 0.0, 0.0]
p1 = [1.0, 0.0, 0.0]
p2 = [1.0, 1.0, 0.0]
p3 = [0.0, 1.0, 0.0]
p4 = [0.0, 0.0, 1.0]
p5 = [1.0, 0.0, 1.0]
p6 = [1.0, 1.0, 0.0]
p7 = [0.0, 1.0, 0.0]
p8 = [0.0, 0.0, 0.0]
p9 = [1, 1.0, 1.0]
p10 = [1, 1.0, 2.0]
points = vtk.vtkPoints()
pid0 = points.InsertNextPoint(p0)
pid1 = points.InsertNextPoint(p1)
pid2 = points.InsertNextPoint(p2)
pid3 = points.InsertNextPoint(p3)
pid4 = points.InsertNextPoint(p4)
pid5 = points.InsertNextPoint(p5)
pid6 = points.InsertNextPoint(p6)
pid7 = points.InsertNextPoint(p7)
pid8 = points.InsertNextPoint(p8)
pid9 = points.InsertNextPoint(p9)
pid10 = points.InsertNextPoint(p10)
# Create the topology of the point (a vertex)
vertices = vtk.vtkCellArray()
lines = vtk.vtkCellArray()
polys = vtk.vtkCellArray()
vertices.InsertNextCell(1)
vertices.InsertCellPoint(pid8)
vertices.InsertNextCell(1)
vertices.InsertCellPoint(pid9)
# create some lines
line = vtk.vtkLine()
line.GetPointIds().SetId(0, pid0)
line.GetPointIds().SetId(1, pid9)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, pid3)
line.GetPointIds().SetId(1, pid10)
lines.InsertNextCell(line)
# create some triangles
tri = vtk.vtkTriangle()
tri.GetPointIds().SetId(0, pid0)
tri.GetPointIds().SetId(1, pid7)
tri.GetPointIds().SetId(2, pid9)
polys.InsertNextCell(tri)
# Create a quad on the four points
quad = vtk.vtkQuad()
quad.GetPointIds().SetId(0, pid0)
quad.GetPointIds().SetId(1, pid1)
quad.GetPointIds().SetId(2, pid2)
quad.GetPointIds().SetId(3, pid3)
quad2 = vtk.vtkQuad()
quad2.GetPointIds().SetId(0, pid4)
quad2.GetPointIds().SetId(1, pid5)
quad2.GetPointIds().SetId(2, pid6)
quad2.GetPointIds().SetId(3, pid7)
polys.InsertNextCell(quad)
polys.InsertNextCell(quad2)
sphere = vtk.vtkSphereSource()
sphere.SetCenter(2, 2, 2)
sphere.SetRadius(1.0)
sp = sphere.GetOutputPort()
sphere.SetPhiResolution(100)
sphere.SetThetaResolution(100)
sphere2 = vtk.vtkSphereSource()
sphere2.SetCenter(-2, -2, -2)
sphere2.SetRadius(1.5)
sp2 = sphere2.GetOutputPort()
sphere2.SetPhiResolution(100)
sphere2.SetThetaResolution(100)
elipse = vtk.vtkParametricEllipsoid()
elipse.SetXRadius(2)
elipse.SetYRadius(3)
elipse.SetZRadius(0.2)
elsource = vtk.vtkParametricFunctionSource()
elsource.SetParametricFunction(elipse)
elsource.Update()
# polys.InsertNextCell(sp)
# Create a polydata object
geodata = vtk.vtkPolyData()
# Set the points and vertices we created as the geometry and topology of the polydata
geodata.SetPoints(points)
geodata.SetVerts(vertices)
geodata.SetPolys(polys)
geodata.SetLines(lines)
geodata.GetPointData().SetScalars(colors)
# Visualize
mappergeo = vtk.vtkPolyDataMapper()
mappersp = vtk.vtkPolyDataMapper()
mappersp2 = vtk.vtkPolyDataMapper()
mapperel = vtk.vtkPolyDataMapper()
mappercont = vtk.vtkPolyDataMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
mappergeo.SetInput(geodata)
else:
mappergeo.SetInputData(geodata)
mappersp.SetInputConnection(sp)
mappersp2.SetInputConnection(sp2)
mapperel.SetInputConnection(elsource.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mappergeo)
actor.GetProperty().SetPointSize(5)
actor.GetProperty().VertexVisibilityOn()
actor.GetProperty().SetVertexColor([0,0,0])
actor2 = vtk.vtkActor()
actor2.SetMapper(mappersp)
actor2.GetProperty().SetColor([0, 0.5, 0.5])
actor.GetProperty().VertexVisibilityOn()
actor.GetProperty().SetVertexColor([0,0,0])
actor2b = vtk.vtkActor()
actor2b.SetMapper(mappersp2)
actor2b.GetProperty().SetColor([0.1, 0.5, 0.1])
actor3 = vtk.vtkActor()
actor3.SetMapper(mapperel)
actor3.SetPosition(1,4,6)
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
WIDTH = 640
HEIGHT = 480
renderWindow.SetSize(WIDTH, HEIGHT)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderer.SetBackground(.9, .9, .9)
renderer.AddActor(actor)
renderer.AddActor(actor2)
renderer.AddActor(actor2b)
renderer.AddActor(actor3)
renderWindow.Render()
renderWindowInteractor.Start()
|
tjssmy/CuviewerPy
|
vtkTests/All.py
|
Python
|
mit
| 4,709
|
[
"VTK"
] |
ea715de5a46a09a384f377b6104c707f38ab8ab9aab42b468d83d142f97c5030
|
from chiplotle.geometry.core.group import Group
from chiplotle.geometry.core.path import Path
from chiplotle.geometry.core.coordinate import Coordinate
from chiplotle.geometry.core.coordinatearray import CoordinateArray
from chiplotle.geometry.transforms.transformvisitor import TransformVisitor
import random
def noise(shape, value):
'''Distort shape by adding noise.
- `value` can be a scalar or a tuple (x, y) that sets the range of the
noise for the x and y coordinates.
'''
def noisify(coords, value):
try:
x, y = value
except TypeError:
x = y = value
result = [ ]
for point in coords:
x_wiggle = random.randrange(-x, x)
y_wiggle = random.randrange(-y, y)
xy = point + Coordinate(x_wiggle, y_wiggle)
result.append(xy)
return CoordinateArray(result)
t = TransformVisitor(noisify)
t.visit(shape, value)
## RUN DEMO CODE
if __name__ == "__main__":
from chiplotle.geometry.shapes.circle import circle
from chiplotle.tools import io
c1 = circle(1000, 100)
c2 = circle(800, 100)
noise(c1, 90)
c1 += Coordinate(1000, 1000)
g = Group([c1, c2])
noise(g, 60)
io.view(g)
|
drepetto/chiplotle
|
chiplotle/geometry/transforms/noise.py
|
Python
|
gpl-3.0
| 1,251
|
[
"VisIt"
] |
b07544ef9ecd892d485cfb90a16b3d605eb878764d137e97d3c5c67c72407d0c
|
"""
Copyright 2015 Hewlett-Packard
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""
import elasticsearch
import logging
import os
from freezer_api.common import _i18n
from freezer_api.common import exceptions as freezer_api_exc
from freezer_api.common import utils
from oslo_config import cfg
from oslo_log import log
CONF = cfg.CONF
LOG = log.getLogger(__name__)
class TypeManager(object):
def __init__(self, es, doc_type, index):
self.es = es
self.index = index
self.doc_type = doc_type
@staticmethod
def get_base_search_filter(user_id, search=None):
search = search or {}
user_id_filter = {"term": {"user_id": user_id}}
base_filter = [user_id_filter]
match_list = [{"match": m} for m in search.get('match', [])]
match_not_list = [{"match": m} for m in search.get('match_not', [])]
base_filter.append({"query": {"bool": {"must": match_list,
"must_not": match_not_list}}})
return base_filter
@staticmethod
def get_search_query(user_id, doc_id, search=None):
search = search or {}
try:
base_filter = TypeManager.get_base_search_filter(user_id, search)
query_filter = {"filter": {"bool": {"must": base_filter}}}
return {'query': {'filtered': query_filter}}
except Exception:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('search operation failed: query not valid'))
def get(self, user_id, doc_id):
try:
res = self.es.get(index=self.index,
doc_type=self.doc_type,
id=doc_id)
doc = res['_source']
except elasticsearch.TransportError:
raise freezer_api_exc.DocumentNotFound(
message=_i18n._('No document found with ID %s') % doc_id)
except Exception as e:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('Get operation failed: %s') % e)
if doc['user_id'] != user_id:
raise freezer_api_exc.AccessForbidden(
_i18n._("Document access forbidden"))
if '_version' in res:
doc['_version'] = res['_version']
return doc
def search(self, user_id, doc_id=None, search=None, offset=0, limit=10):
search = search or {}
query_dsl = self.get_search_query(user_id, doc_id, search)
try:
res = self.es.search(index=self.index, doc_type=self.doc_type,
size=limit, from_=offset, body=query_dsl)
except elasticsearch.ConnectionError:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('unable to connect to db server'))
except Exception as e:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('search operation failed: %s') % e)
hit_list = res['hits']['hits']
return [x['_source'] for x in hit_list]
def insert(self, doc, doc_id=None):
try:
# remove _version from the document
doc.pop('_version', None)
res = self.es.index(index=self.index, doc_type=self.doc_type,
body=doc, id=doc_id)
created = res['created']
version = res['_version']
self.es.indices.refresh(index=self.index)
except elasticsearch.TransportError as e:
if e.status_code == 409:
raise freezer_api_exc.DocumentExists(message=e.error)
raise freezer_api_exc.StorageEngineError(
message=_i18n._('index operation failed %s') % e)
except Exception as e:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('index operation failed %s') % e)
return (created, version)
def delete(self, user_id, doc_id):
query_dsl = self.get_search_query(user_id, doc_id)
try:
results = self.es.search(index=self.index,
doc_type=self.doc_type,
body=query_dsl)
results = results['hits']['hits']
except Exception as e:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('Scan operation failed: %s') % e)
id = None
for res in results:
id = res.get('_id')
try:
self.es.delete(index=self.index, doc_type=self.doc_type, id=id)
self.es.indices.refresh(index=self.index)
except Exception as e:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('Delete operation failed: %s') % e)
return id
class BackupTypeManager(TypeManager):
def __init__(self, es, doc_type, index='freezer'):
TypeManager.__init__(self, es, doc_type, index=index)
@staticmethod
def get_search_query(user_id, doc_id, search=None):
search = search or {}
base_filter = TypeManager.get_base_search_filter(user_id, search)
if doc_id is not None:
base_filter.append({"term": {"backup_id": doc_id}})
if 'time_after' in search:
base_filter.append(
{"range": {"timestamp": {"gte": int(search['time_after'])}}}
)
if 'time_before' in search:
base_filter.append(
{"range": {"timestamp": {"lte": int(search['time_before'])}}}
)
query_filter = {"filter": {"bool": {"must": base_filter}}}
return {'query': {'filtered': query_filter}}
class ClientTypeManager(TypeManager):
def __init__(self, es, doc_type, index='freezer'):
TypeManager.__init__(self, es, doc_type, index=index)
@staticmethod
def get_search_query(user_id, doc_id, search=None):
search = search or {}
base_filter = TypeManager.get_base_search_filter(user_id, search)
if doc_id is not None:
base_filter.append({"term": {"client.client_id": doc_id}})
query_filter = {"filter": {"bool": {"must": base_filter}}}
return {'query': {'filtered': query_filter}}
class JobTypeManager(TypeManager):
def __init__(self, es, doc_type, index='freezer'):
TypeManager.__init__(self, es, doc_type, index=index)
@staticmethod
def get_search_query(user_id, doc_id, search=None):
search = search or {}
base_filter = TypeManager.get_base_search_filter(user_id, search)
if doc_id is not None:
base_filter.append({"term": {"job_id": doc_id}})
query_filter = {"filter": {"bool": {"must": base_filter}}}
return {'query': {'filtered': query_filter}}
def update(self, job_id, job_update_doc):
# remove _version from the document
job_update_doc.pop('_version', 0)
update_doc = {"doc": job_update_doc}
try:
res = self.es.update(index=self.index, doc_type=self.doc_type,
id=job_id, body=update_doc)
version = res['_version']
self.es.indices.refresh(index=self.index)
except elasticsearch.TransportError as e:
if e.status_code == 409:
raise freezer_api_exc.DocumentExists(message=e.error)
raise freezer_api_exc.DocumentNotFound(
message=_i18n._('Unable to find job to update '
'with id %(id)s. %(e)s') % {'id': job_id,
'e': e})
except Exception:
raise freezer_api_exc.StorageEngineError(
message=_i18n._('Unable to update job with id %s') % job_id)
return version
class ActionTypeManager(TypeManager):
def __init__(self, es, doc_type, index='freezer'):
TypeManager.__init__(self, es, doc_type, index=index)
@staticmethod
def get_search_query(user_id, doc_id, search=None):
search = search or {}
base_filter = TypeManager.get_base_search_filter(user_id, search)
if doc_id is not None:
base_filter.append({"term": {"action_id": doc_id}})
query_filter = {"filter": {"bool": {"must": base_filter}}}
return {'query': {'filtered': query_filter}}
def update(self, action_id, action_update_doc):
# remove _version from the document
action_update_doc.pop('_version', 0)
update_doc = {"doc": action_update_doc}
try:
res = self.es.update(index=self.index, doc_type=self.doc_type,
id=action_id, body=update_doc)
version = res['_version']
self.es.indices.refresh(index=self.index)
except elasticsearch.TransportError as e:
if e.status_code == 409:
raise freezer_api_exc.DocumentExists(message=e.error)
raise freezer_api_exc.DocumentNotFound(
message=_i18n._('Unable to find action to update '
'with id %s') % action_id)
except Exception:
raise freezer_api_exc.StorageEngineError(
message=_i18n._(
'Unable to update action with id %s') % action_id)
return version
class SessionTypeManager(TypeManager):
def __init__(self, es, doc_type, index='freezer'):
TypeManager.__init__(self, es, doc_type, index=index)
@staticmethod
def get_search_query(user_id, doc_id, search=None):
search = search or {}
base_filter = TypeManager.get_base_search_filter(user_id, search)
if doc_id is not None:
base_filter.append({"term": {"session_id": doc_id}})
query_filter = {"filter": {"bool": {"must": base_filter}}}
return {'query': {'filtered': query_filter}}
def update(self, session_id, session_update_doc):
# remove _version from the document
session_update_doc.pop('_version', 0)
update_doc = {"doc": session_update_doc}
try:
res = self.es.update(index=self.index, doc_type=self.doc_type,
id=session_id, body=update_doc)
version = res['_version']
self.es.indices.refresh(index=self.index)
except elasticsearch.TransportError as e:
if e.status_code == 409:
raise freezer_api_exc.DocumentExists(message=e.error)
raise freezer_api_exc.DocumentNotFound(
message=_i18n._('Unable to update session '
'%(id)s %(e)s') % {'id': session_id, 'e': e}
)
except Exception:
raise freezer_api_exc.StorageEngineError(
message=_i18n._(
'Unable to update session with id %s') % session_id)
return version
class ElasticSearchEngine(object):
_OPTS = [
cfg.ListOpt('hosts',
default=['http://127.0.0.1:9200'],
help='specify the storage hosts'),
cfg.StrOpt('index',
default='freezer',
help='specify the name of the elasticsearch index'),
cfg.IntOpt('timeout',
default=60,
help='specify the connection timeout'),
cfg.IntOpt('retries',
default=20,
help='number of retries to allow before raising and error'),
cfg.BoolOpt('use_ssl',
default=False,
help='explicitly turn on SSL'),
cfg.BoolOpt('verify_certs',
default=False,
help='turn on SSL certs verification'),
cfg.StrOpt('ca_certs',
help='path to CA certs on disk'),
cfg.IntOpt('number_of_replicas',
default=0,
help='Number of replicas for elk cluster. Default is 0. '
'Use 0 for no replicas. This should be set to (number '
'of node in the ES cluter -1).')
]
def __init__(self, backend):
"""backend: name of the section in the config file to load
elasticsearch opts
"""
self.index = None
self.es = None
self.backup_manager = None
self.client_manager = None
self.job_manager = None
self.action_manager = None
self.session_manager = None
# register elasticsearch opts
CONF.register_opts(self._OPTS, group=backend)
self.conf = dict(CONF.get(backend))
self.backend = backend
self._validate_opts()
self.init(**self.conf)
def _validate_opts(self):
if not 'hosts' or 'endpoint' in self.conf.keys():
raise ValueError("Couldn't find hosts in {0} section".format(
self.backend)
)
if self.conf.get('ca_certs'):
if not os.path.isfile(self.conf.get('ca_certs')):
raise Exception("File not found: ca_certs file ({0}) not "
"found".format(self.conf.get('ca_certs')))
def get_opts(self):
return self._OPTS
def init(self, index='freezer', **kwargs):
self.index = index
self.es = elasticsearch.Elasticsearch(**kwargs)
logging.info('Storage backend: Elasticsearch '
'at %s' % kwargs['hosts'])
self.backup_manager = BackupTypeManager(self.es, 'backups')
self.client_manager = ClientTypeManager(self.es, 'clients')
self.job_manager = JobTypeManager(self.es, 'jobs')
self.action_manager = ActionTypeManager(self.es, 'actions')
self.session_manager = SessionTypeManager(self.es, 'sessions')
def get_backup(self, user_id, backup_id):
return self.backup_manager.get(user_id, backup_id)
def search_backup(self, user_id, offset=0, limit=10, search=None):
search = search or {}
return self.backup_manager.search(user_id,
search=search,
offset=offset,
limit=limit)
def add_backup(self, user_id, user_name, doc):
# raises if data is malformed (HTTP_400) or already present (HTTP_409)
backup_metadata_doc = utils.BackupMetadataDoc(user_id, user_name, doc)
if not backup_metadata_doc.is_valid():
raise freezer_api_exc.BadDataFormat(
message=_i18n._('Bad Data Format'))
backup_id = backup_metadata_doc.backup_id
self.backup_manager.insert(backup_metadata_doc.serialize(), backup_id)
return backup_id
def delete_backup(self, user_id, backup_id):
return self.backup_manager.delete(user_id, backup_id)
def get_client(self, user_id, client_id=None,
offset=0, limit=10, search=None):
search = search or {}
return self.client_manager.search(user_id,
client_id,
search=search,
offset=offset,
limit=limit)
def add_client(self, user_id, doc):
client_doc = utils.ClientDoc.create(doc, user_id)
client_id = client_doc['client']['client_id']
existing = self.client_manager.search(user_id, client_id)
if existing:
raise freezer_api_exc.DocumentExists(
message=_i18n._(
'Client already registered with ID %s') % client_id)
self.client_manager.insert(client_doc)
logging.info('Client registered, client_id: %s' % client_id)
return client_id
def delete_client(self, user_id, client_id):
return self.client_manager.delete(user_id, client_id)
def get_job(self, user_id, job_id):
return self.job_manager.get(user_id, job_id)
def search_job(self, user_id, offset=0, limit=10, search=None):
search = search or {}
return self.job_manager.search(user_id,
search=search,
offset=offset,
limit=limit)
def add_job(self, user_id, doc):
jobdoc = utils.JobDoc.create(doc, user_id)
job_id = jobdoc['job_id']
self.job_manager.insert(jobdoc, job_id)
logging.info('Job registered, job id: %s' % job_id)
return job_id
def delete_job(self, user_id, job_id):
return self.job_manager.delete(user_id, job_id)
def update_job(self, user_id, job_id, patch_doc):
valid_patch = utils.JobDoc.create_patch(patch_doc)
# check that document exists
assert (self.job_manager.get(user_id, job_id))
version = self.job_manager.update(job_id, valid_patch)
logging.info('Job %(id)s updated to version %(version)s' %
{'id': job_id, 'version': version})
return version
def replace_job(self, user_id, job_id, doc):
# check that no document exists with
# same job_id and different user_id
try:
self.job_manager.get(user_id, job_id)
except freezer_api_exc.DocumentNotFound:
pass
valid_doc = utils.JobDoc.update(doc, user_id, job_id)
(created, version) = self.job_manager.insert(valid_doc, job_id)
if created:
logging.info('Job %s created' % job_id)
else:
logging.info(
'Job %(id)s replaced with version %(version)s' %
{'id': job_id, 'version': version})
return version
def get_action(self, user_id, action_id):
return self.action_manager.get(user_id, action_id)
def search_action(self, user_id, offset=0, limit=10, search=None):
search = search or {}
return self.action_manager.search(user_id,
search=search,
offset=offset,
limit=limit)
def add_action(self, user_id, doc):
actiondoc = utils.ActionDoc.create(doc, user_id)
action_id = actiondoc['action_id']
self.action_manager.insert(actiondoc, action_id)
logging.info('Action registered, action id: %s' % action_id)
return action_id
def delete_action(self, user_id, action_id):
return self.action_manager.delete(user_id, action_id)
def update_action(self, user_id, action_id, patch_doc):
valid_patch = utils.ActionDoc.create_patch(patch_doc)
# check that document exists
assert (self.action_manager.get(user_id, action_id))
version = self.action_manager.update(action_id, valid_patch)
logging.info(
'Action %(id)s updated to version %(version)s' %
{'id': action_id, 'version': version})
return version
def replace_action(self, user_id, action_id, doc):
# check that no document exists with
# same action_id and different user_id
try:
self.action_manager.get(user_id, action_id)
except freezer_api_exc.DocumentNotFound:
pass
valid_doc = utils.ActionDoc.update(doc, user_id, action_id)
(created, version) = self.action_manager.insert(valid_doc, action_id)
if created:
logging.info('Action %s created' % action_id)
else:
logging.info(
'Action %(id)s replaced with version %(version)s'
% {'id': action_id, 'version': version})
return version
def get_session(self, user_id, session_id):
return self.session_manager.get(user_id, session_id)
def search_session(self, user_id, offset=0, limit=10, search=None):
search = search or {}
return self.session_manager.search(user_id,
search=search,
offset=offset,
limit=limit)
def add_session(self, user_id, doc):
session_doc = utils.SessionDoc.create(doc, user_id)
session_id = session_doc['session_id']
self.session_manager.insert(session_doc, session_id)
logging.info(
'Session registered, session id: %s' % session_id)
return session_id
def delete_session(self, user_id, session_id):
return self.session_manager.delete(user_id, session_id)
def update_session(self, user_id, session_id, patch_doc):
valid_patch = utils.SessionDoc.create_patch(patch_doc)
# check that document exists
assert (self.session_manager.get(user_id, session_id))
version = self.session_manager.update(session_id, valid_patch)
logging.info(
'Session %(id)s updated to version %(version)s' %
{'id': session_id, 'version': version})
return version
def replace_session(self, user_id, session_id, doc):
# check that no document exists with
# same session_id and different user_id
try:
self.session_manager.get(user_id, session_id)
except freezer_api_exc.DocumentNotFound:
pass
valid_doc = utils.SessionDoc.update(doc, user_id, session_id)
(created, version) = self.session_manager.insert(valid_doc, session_id)
if created:
logging.info('Session %s created' % session_id)
else:
logging.info(
'Session %(id)s replaced with version %(version)s'
% {'id': session_id, 'version': version})
return version
|
szaher/freezer-api
|
freezer_api/storage/elastic.py
|
Python
|
apache-2.0
| 22,193
|
[
"Elk"
] |
98d4800d8f3166f3bf8c0ae111cfafa8cb998c2cfd44528579c2c17cc2189789
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#******************************************************************************
#*
#* Copyright (C) 2015 Kiran Karra <kiran.karra@gmail.com>
#*
#* This program is free software: you can redistribute it and/or modify
#* it under the terms of the GNU General Public License as published by
#* the Free Software Foundation, either version 3 of the License, or
#* (at your option) any later version.
#*
#* This program is distributed in the hope that it will be useful,
#* but WITHOUT ANY WARRANTY; without even the implied warranty of
#* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#* GNU General Public License for more details.
#*
#* You should have received a copy of the GNU General Public License
#* along with this program. If not, see <http://www.gnu.org/licenses/>.
#******************************************************************************
import math
import numpy as np
from debye import debye
from scipy.optimize import fsolve
from copulastat import copulastat
"""
invcopulastat.py contains routines which provide the inverse copula dependency
measures the copula family type and the copula's specific dependency parameter.
The relationships used in the functions are well known, and documented in
many copula research papers, including Nelsen's Introduction to Copula's.
"""
def invcopulastat(family, dependency, val):
dependency_lc = dependency.lower()
if(dependency_lc!='kendall' and dependency_lc!='spearman'):
raise ValueError('Invalid dependency argument -- must be kendall or spearman')
if(family.lower()=='gaussian'):
r = _gaussian(dependency_lc, val)
elif(family.lower()=='t'):
r = _t(dependency_lc, val)
elif(family.lower()=='clayton'):
r = _clayton(dependency_lc, val)
elif(family.lower()=='gumbel'):
r = _gumbel(dependency_lc, val)
elif(family.lower()=='frank'):
r = _frank(dependency_lc, val)
else:
raise ValueError('Unsupported Copula Family!')
return r
def _gaussian(dependency, val):
if(dependency=='kendall'):
r = np.sin(math.pi/2.0*val)
elif(dependency=='spearman'):
r = 2*np.sin(math.pi/6.0*val)
return r
def _t(dependency, val):
if(dependency=='kendall'):
r = np.sin(math.pi/2.0*val)
elif(dependency=='spearman'):
r = 2*np.sin(math.pi/6.0*val)
return r
def _clayton(dependency, val):
if(dependency=='kendall'):
if(val<0 or val>=1):
raise ValueError('Valid values of Kendall\'s Tau for the Clayton Copula are [0,1)')
d = 2.0*val/(1.0-val)
elif(dependency=='spearman'):
raise NotImplementedError('Spearmans Rho currently unsupported for Clayton Copula family!')
return d
def _gumbel(dependency, val):
if(dependency=='kendall'):
if(val<0 or val>=1):
raise ValueError('Valid values of Kendall\'s Tau for the Gumbel Copula are [0,1)')
d = 1.0/(1.0-val)
elif(dependency=='spearman'):
raise NotImplementedError('Spearmans Rho currently unsupported for Gumbel Copula family!')
return d
def _frank_kendall_fopt(alpha, tau):
return 4*( debye(alpha,1) - 1 )/alpha + 1 - tau
def _frank(dependency, val):
if(dependency=='kendall'):
return fsolve(_frank_kendall_fopt, 1, args=(val))[0]
elif(dependency=='spearman'):
# TODO -- use function solvers in scipy to invert debye function for the closed form solution
raise NotImplementedError('Spearmans Rho currently unsupported for Frank Copula family!')
return r
def test_python_vs_matlab(family):
# DISCLAIMER: this code assumes copulastat is working properly and tested
if(family.lower()=='gaussian'):
dependency = 'kendall'
rho = 0.3
rho_calc = invcopulastat(family, dependency, copulastat(family, dependency, rho))
p1 = np.isclose(rho, rho_calc)
rho = 0.7
rho_calc = invcopulastat(family, dependency, copulastat(family, dependency, rho))
p2 = np.isclose(rho, rho_calc)
dependency = 'spearman'
rho = 0.3
rho_calc = invcopulastat(family, dependency, copulastat(family, dependency, rho))
p3 = np.isclose(rho, rho_calc)
rho = 0.7
rho_calc = invcopulastat(family, dependency, copulastat(family, dependency, rho))
p4 = np.isclose(rho, rho_calc)
if(p1 and p2 and p3 and p4):
print 'Gaussian CopulaStat tests PASSED!'
else:
print 'Gaussian CopulaStat tests FAILED!'
elif(family.lower()=='t'):
pass
elif(family.lower()=='clayton' or family.lower()=='gumbel' or family.lower()=='frank'):
dependency = 'kendall'
alpha = 0.3
tau = copulastat(family, dependency, alpha)
alpha_calc = invcopulastat(family, dependency, tau)
p1 = np.isclose(alpha, alpha_calc)
alpha = 0.7
tau = copulastat(family, dependency, alpha)
alpha_calc = invcopulastat(family, dependency, tau)
p2 = np.isclose(alpha, alpha_calc)
if(p1 and p2):
print family + ' CopulaStat tests PASSED!'
else:
print family + ' CopulaStat tests FAILED!'
if __name__=='__main__':
test_python_vs_matlab('Gaussian')
test_python_vs_matlab('Clayton')
test_python_vs_matlab('Gumbel')
test_python_vs_matlab('Frank')
|
kkarrancsu/copula-bayesian-networks
|
invcopulastat.py
|
Python
|
gpl-3.0
| 5,492
|
[
"Gaussian"
] |
4d3711af8fb1717a6908a7e04672297bba917cb4d6eac9203d58144ca3c189dc
|
"""
It is used to compile the web framework
"""
import os
import tempfile
import shutil
import subprocess
import gzip
import sys
from DIRAC import gLogger, gConfig, rootPath, S_OK, S_ERROR
from DIRAC.Core.Utilities.CFG import CFG
__RCSID__ = "$Id$"
class WebAppCompiler(object):
def __init__(self, params):
self.__params = params
self.__extVersion = '4.2.1.883'
self.__extDir = 'extjs' # this directory will contain all the resources required by ExtJS
self.__sdkDir = params.extjspath if self.__params.extjspath is not None else '/opt/dirac/extjs/ext-4.2.1.883'
self.__webAppPath = os.path.join(self.__params.destination, 'WebAppDIRAC', 'WebApp')
self.__staticPaths = [os.path.join(self.__webAppPath, 'static')]
if self.__params.name != 'WebAppDIRAC':
self.__staticPaths.append(os.path.join(self.__params.destination, self.__params.name, 'WebApp', 'static'))
self.__classPaths = [os.path.join(self.__webAppPath, *p) for p in (("static", "core", "js", "utils"),
("static", "core", "js", "core"))]
self.__extjsDirsToCopy = []
self.__extjsFilesToCopy = []
if self.__extVersion in self.__sdkDir:
self.__classPaths.append(os.path.join(os.path.dirname(self.__sdkDir), "examples", "ux"))
self.__classPaths.append(os.path.join(os.path.dirname(self.__sdkDir), "examples", "ux", "form"))
self.__sdkPath = os.path.join(self.__sdkDir, "src")
self.__extjsDirsToCopy.append(os.path.join(os.path.dirname(self.__sdkDir), "resources"))
self.__extjsFilesToCopy.append(os.path.join(os.path.dirname(self.__sdkDir), "ext-all-dev.js"))
else:
self.__classPaths.append(os.path.join(os.path.dirname(self.__sdkDir), "build/ext-all-debug.js"))
self.__classPaths.append(os.path.join(os.path.dirname(self.__sdkDir), "build/packages/ux/classic/ux-debug.js"))
self.__classPaths.append(
os.path.join(os.path.dirname(self.__sdkDir), "build/packages/charts/classic/charts-debug.js"))
self.__sdkPath = self.__sdkDir
self.__extjsDirsToCopy.append(os.path.join(os.path.dirname(self.__sdkDir), "build/packages"))
self.__extjsDirsToCopy.append(os.path.join(os.path.dirname(self.__sdkDir), "build/classic"))
self.__extjsFilesToCopy.append(os.path.join(os.path.dirname(self.__sdkDir), "build/ext-all.js"))
self.__extjsFilesToCopy.append(os.path.join(os.path.dirname(self.__sdkDir), "build/ext-all-debug.js"))
self.__extjsFilesToCopy.append(
os.path.join(os.path.dirname(self.__sdkDir), "build/packages/ux/classic/ux-debug.js"))
self.__debugFlag = str(gLogger.getLevel() in ('DEBUG', 'VERBOSE', 'INFO')).lower()
self.__compileTemplate = os.path.join(self.__params.destination, 'WebAppDIRAC', "Lib", "CompileTemplates")
# this place will be used, if sencha cmd is not available
self.__senchacmddir = os.path.join(rootPath, "sbin", "Sencha", "Cmd")
self.__senchaVersion = "v6.5.0.180"
self.__appDependency = {}
self.__dependencySection = "Dependencies"
def __deployResources(self):
"""
This method copy the required files and directories to the appropriate place
"""
extjsDirPath = os.path.join(self.__webAppPath, 'static', self.__extDir)
if not os.path.exists(extjsDirPath):
try:
os.mkdir(extjsDirPath)
except OSError as e:
gLogger.error("Can not create release extjs", repr(e))
return S_ERROR("Can not create release extjs" + repr(e))
for dirSrc in self.__extjsDirsToCopy:
try:
shutil.copytree(dirSrc, os.path.join(extjsDirPath, os.path.split(dirSrc)[1]))
except OSError as e:
if e.errno != 17:
errorMsg = "Can not copy %s directory to %s: %s" % (
dirSrc, os.path.join(extjsDirPath, os.path.split(dirSrc)[1]), repr(e))
gLogger.error(errorMsg)
return S_ERROR(errorMsg)
else:
gLogger.warn("%s directory is already exists. It will be not overwritten!" %
os.path.join(extjsDirPath, os.path.split(dirSrc)[1]))
for filePath in self.__extjsFilesToCopy:
try:
shutil.copy(filePath, extjsDirPath)
except (IOError, OSError) as e:
errorMsg = "Can not copy %s file to %s: %s" % (filePath, extjsDirPath, repr(e))
gLogger.warn(errorMsg)
return S_OK()
def __writeINFile(self, tplName, extra=False):
"""
It creates a temporary file using different templates. For example: /tmp/zmathe/tmp4sibR5.compilejs.app.tpl
This is required to compile the web framework.
:params str tplName: it is the name of the template
:params dict extra: it contains the application location, which will be added to the temporary file
:return: the location of the file
"""
inTpl = os.path.join(self.__compileTemplate, tplName)
try:
with open(inTpl) as infd:
data = infd.read()
except IOError:
return S_ERROR("%s does not exist" % inTpl)
data = data.replace("%EXT_VERSION%", self.__extVersion)
if extra:
for k in extra:
data = data.replace("%%%s%%" % k.upper(), extra[k])
outfd, filepath = tempfile.mkstemp(".compilejs.%s" % tplName)
os.write(outfd, data)
os.close(outfd)
return S_OK(filepath)
def __cmd(self, cmd):
"""
This is used to execure a command
:params list cmd: sencha command which will be executed
"""
env = {}
for k in ('LD_LIBRARY_PATH', 'DYLD_LIBRARY_PATH'):
if k in os.environ:
env[k] = os.environ[k]
os.environ.pop(k)
gLogger.verbose("Command is: %s" % " ".join(cmd))
try:
result = subprocess.call(cmd)
except OSError as e:
message = 'Command does not exists: %s -> %s' % (','.join(cmd), e)
gLogger.error(message)
return S_ERROR(message)
for k in env:
os.environ[k] = env[k]
return result
def __compileApp(self, extPath, extName, appName, extClassPath=""):
"""
It compiles an application
:param str extPath: directory full path, which contains the applications
for example: /tmp/zmathe/tmpFxr5LzDiracDist/WebAppDIRAC/WebApp/static/DIRA
:param str extName: the name of the application for example: DIRAC or LHCbDIRAC, etc
:param str appName: the name of the application for example: Accounting
:param str extClassPath: if we compile an extension, we can provide the class path of the base class
"""
result = self.__writeINFile("app.tpl", {'APP_LOCATION': '%s.%s.classes.%s' % (extName, appName, appName)})
if not result['OK']:
return result
inFile = result['Value']
buildDir = os.path.join(extPath, appName, 'build')
try:
shutil.rmtree(buildDir)
except OSError:
pass
if not os.path.isdir(buildDir):
try:
os.makedirs(buildDir)
except IOError, excp:
return S_ERROR("Can't create build dir %s" % excp)
outFile = os.path.join(buildDir, "index.html")
compressedJsFile = os.path.join(buildDir, appName + '.js')
classPath = list(self.__classPaths)
excludePackage = ",%s.*" % extName
if extClassPath != "":
classPath.append(extClassPath)
excludePackage = ",DIRAC.*,%s.*" % extName
classPath.append(os.path.join(extPath, appName, "classes"))
cmd = ['sencha', '-sdk', self.__sdkPath, 'compile', '-classpath=%s' % ",".join(classPath),
'page', '-name=page', '-input-file', inFile, '-out', outFile, 'and',
'restore', 'page', 'and', 'exclude', '-not', '-namespace', 'Ext.dirac.*%s' % excludePackage, 'and',
'concat', '-yui', compressedJsFile]
if self.__cmd(cmd):
return S_ERROR("Error compiling %s.%s" % (extName, appName))
return S_OK()
def __zip(self, staticPath, stack=""):
"""
It compress the compiled applications
"""
c = 0
l = "|/-\\"
for entry in os.listdir(staticPath):
n = stack + l[c % len(l)]
if entry[-3:] == ".gz":
continue
ePath = os.path.join(staticPath, entry)
if os.path.isdir(ePath):
self.__zip(ePath, n)
continue
zipPath = "%s.gz" % ePath
if os.path.isfile(zipPath):
if os.stat(zipPath).st_mtime > os.stat(ePath).st_mtime:
continue
print "%s%s\r" % (n, " " * (20 - len(n))),
c += 1
inf = gzip.open(zipPath, "wb", 9)
with open(ePath, "rb") as outf:
buf = outf.read(8192)
while buf:
inf.write(buf)
buf = outf.read(8192)
inf.close()
def run(self):
"""
This compiles the web framework
"""
# if the sencha does not installed, it will exit
self.__checkSenchacmd()
retVal = self.__deployResources()
if not retVal['OK']:
return retVal
# we are compiling an extension of WebAppDIRAC
if self.__params.name != 'WebAppDIRAC':
self.__appDependency.update(self.getAppDependencies())
staticPath = os.path.join(self.__webAppPath, "static")
gLogger.notice("Compiling core: %s" % staticPath)
result = self.__writeINFile("core.tpl")
if not result['OK']:
return result
inFile = result['Value']
buildDir = os.path.join(staticPath, "core", "build")
try:
shutil.rmtree(buildDir)
except OSError:
pass
outFile = os.path.join(staticPath, "core", "build", "index.html")
gLogger.verbose(" IN file written to %s" % inFile)
cmd = ['sencha', '-sdk', self.__sdkPath, 'compile', '-classpath=%s' % ",".join(self.__classPaths),
'page', '-yui', '-input-file', inFile, '-out', outFile]
if self.__cmd(cmd):
gLogger.error("Error compiling JS")
return S_ERROR("Failed compiling core")
try:
os.unlink(inFile)
except IOError:
pass
for staticPath in self.__staticPaths:
gLogger.notice("Looing into %s" % staticPath)
extDirectoryContent = os.listdir(staticPath)
if len(extDirectoryContent) == 0:
return S_ERROR("The extension directory is empty:" + str(staticPath))
else:
extNames = [ext for ext in extDirectoryContent if 'DIRAC' in ext]
if len(extNames) > 1:
extNames.remove('DIRAC')
extName = extNames[-1]
gLogger.notice("Detected extension:%s" % extName)
extPath = os.path.join(staticPath, extName)
if not os.path.isdir(extPath):
continue
gLogger.notice("Exploring %s" % extName)
for appName in os.listdir(extPath):
expectedJS = os.path.join(extPath, appName, "classes", "%s.js" % appName)
if not os.path.isfile(expectedJS):
continue
classPath = self.__getClasspath(extName, appName)
gLogger.notice("Trying to compile %s.%s.classes.%s CLASSPATH=%s" % (extName, appName, appName, classPath))
result = self.__compileApp(extPath, extName, appName, classPath)
if not result['OK']:
return result
gLogger.notice("Zipping static files")
self.__zip(staticPath)
gLogger.notice("Done")
return S_OK()
def __getClasspath(self, extName, appName):
classPath = ''
dependency = self.__appDependency.get("%s.%s" % (extName, appName), "")
if dependency != "":
depPath = dependency.split(".")
for staticPath in self.__staticPaths:
expectedJS = os.path.join(staticPath, depPath[0], depPath[1], "classes")
gLogger.notice(expectedJS)
if not os.path.isdir(expectedJS):
continue
classPath = expectedJS
return classPath
def __checkSenchacmd(self):
"""
Before we start the distribution the sencha cmd must be checked
"""
try:
self.__cmd(["sencha"])
except OSError, _:
try:
path = os.path.join(self.__senchacmddir, self.__senchaVersion)
if os.path.exists(path):
sys.path.append(path)
syspath = os.environ['PATH']
os.environ['PATH'] = path + os.pathsep + syspath
except OSError, _:
raise OSError("sencha cmd is not installed!")
def getAppDependencies(self):
"""
Generate the dependency dictionary
:return: Dict
"""
if self.__params.name != 'WebAppDIRAC':
self._loadWebAppCFGFiles(self.__params.name)
dependency = {}
fullName = "%s/%s" % ("/WebApp", self.__dependencySection)
result = gConfig.getOptions(fullName)
if not result['OK']:
gLogger.error(result['Message'])
return dependency
optionsList = result['Value']
for opName in optionsList:
opVal = gConfig.getValue("%s/%s" % (fullName, opName))
dependency[opName] = opVal
return dependency
def _loadWebAppCFGFiles(self, extension):
"""
Load WebApp/web.cfg definitions
:param str extension: the module name of the extension of WebAppDirac for example: LHCbWebDIRAC
"""
exts = [extension, "WebAppDIRAC"]
webCFG = CFG()
for modName in reversed(exts):
cfgPath = os.path.join(self.__params.destination, "%s/WebApp" % modName, "web.cfg")
if not os.path.isfile(cfgPath):
gLogger.verbose("Web configuration file %s does not exists!" % cfgPath)
continue
try:
modCFG = CFG().loadFromFile(cfgPath)
except Exception, excp:
gLogger.error("Could not load %s: %s" % (cfgPath, excp))
continue
gLogger.verbose("Loaded %s" % cfgPath)
expl = ["/WebApp"]
while len(expl):
current = expl.pop(0)
if not modCFG.isSection(current):
continue
if modCFG.getOption("%s/AbsoluteDefinition" % current, False):
gLogger.verbose("%s:%s is an absolute definition" % (modName, current))
try:
webCFG.deleteKey(current)
except:
pass
modCFG.deleteKey("%s/AbsoluteDefinition" % current)
else:
for sec in modCFG[current].listSections():
expl.append("%s/%s" % (current, sec))
# Add the modCFG
webCFG = webCFG.mergeWith(modCFG)
gConfig.loadCFG(webCFG)
|
andresailer/DIRAC
|
FrameworkSystem/Client/WebAppCompiler.py
|
Python
|
gpl-3.0
| 13,996
|
[
"DIRAC"
] |
e964183274100cee2163fc370de307adc809127d543792efb0fa86454bfcdb79
|
# -*- coding: utf-8 -*-
#
# multimeter_file.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# NEST is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
'''
Multimeter to file example
--------------------------
This file demonstrates recording from an `iaf_cond_alpha` neuron using a
multimeter and writing data to file.
'''
'''
First, the necessary modules for simulation and plotting are imported.
The simulation kernel is put back to its initial state using `ResetKernel`.
'''
import nest
import numpy
import pylab
nest.ResetKernel()
'''
With `SetKernelStatus`, global properties of the simulation kernel can be
specified. The following properties are related to writing to file:
* `overwrite_files` is set to True to permit overwriting of an existing file.
* `data_path` is the path to which all data is written. It is given relative to
the current working directory.
* 'data_prefix' allows to specify a common prefix for all data files.
'''
nest.SetKernelStatus({"overwrite_files": True,
"data_path": "",
"data_prefix": ""})
'''
For illustration, the recordables of the `iaf_cond_alpha` neuron model are
displayed. This model is an implementation of a spiking neuron using
integrate-and-fire dynamics with conductance-based synapses. Incoming spike
events induce a post-synaptic change of conductance modelled by an alpha
function.
'''
print("iaf_cond_alpha recordables: {0}".format( \
nest.GetDefaults("iaf_cond_alpha")["recordables"]))
'''
A neuron, a multimeter as recording device and two spike generators for
excitatory and inhibitory stimulation are instantiated. The command `Create`
expects a model type and, optionally, the desired number of nodes and a
dictionary of parameters to overwrite the default values of the model.
* For the neuron, the rise time of the excitatory synaptic alpha function
in ms `tau_syn_ex` and the reset potential of the membrane in mV `V_reset`
are specified.
* For the multimeter, the time interval for recording in ms `interval` and a
selection of measures to record (the membrane voltage in mV `V_m` and the
excitatory `g_ex` and inhibitoy `g_in` synaptic conductances in nS) are set.
In addition, more parameters can be modified for writing to file:
- `withgid` is set to True to record the global id of the observed node(s).
(default: False).
- `to_file` indicates whether to write the recordings to file and is set
to True.
- `label` specifies an arbitrary label for the device. It is used instead of
the name of the model in the output file name.
* For the spike generators, the spike times in ms `spike_times` are given
explicitly.
'''
n = nest.Create("iaf_cond_alpha",
params = {"tau_syn_ex": 1.0, "V_reset": -70.0})
m = nest.Create("multimeter",
params = {"interval": 0.1,
"record_from": ["V_m", "g_ex", "g_in"],
"withgid": True,
"to_file": True,
"label": "my_multimeter"})
s_ex = nest.Create("spike_generator",
params = {"spike_times": numpy.array([10.0, 20.0, 50.0])})
s_in = nest.Create("spike_generator",
params = {"spike_times": numpy.array([15.0, 25.0, 55.0])})
'''
Next, the spike generators are connected to the neuron with `Connect`. Synapse
specifications can be provided in a dictionary. In this example of a
conductance-based neuron, the synaptic weight `weight` is given in nS. Note that
it is positive for excitatory and negative for inhibitory connections.
'''
nest.Connect(s_ex, n, syn_spec={"weight": 40.0})
nest.Connect(s_in, n, syn_spec={"weight": -20.0})
nest.Connect(m, n)
'''
A network simulation with a duration of 100 ms is started with `Simulate`.
'''
nest.Simulate(100.)
'''
After the simulation, the recordings are obtained from the multimeter via the
key `events` of the status dictionary accessed by `GetStatus`. `times` indicates
the recording times stored for each data point. They are recorded if the
parameter `withtime` of the multimeter is set to True which is the default case.
'''
events = nest.GetStatus(m)[0]["events"]
t = events["times"];
'''
Finally, the time courses of the membrane voltage and the synaptic
conductance are displayed.
'''
pylab.clf()
pylab.subplot(211)
pylab.plot(t, events["V_m"])
pylab.axis([0, 100, -75, -53])
pylab.ylabel("membrane potential (mV)")
pylab.subplot(212)
pylab.plot(t, events["g_ex"], t, events["g_in"])
pylab.axis([0, 100, 0, 45])
pylab.xlabel("time (ms)")
pylab.ylabel("synaptic conductance (nS)")
pylab.legend(("g_exc", "g_inh"))
|
uahic/nest-simulator
|
pynest/examples/multimeter_file.py
|
Python
|
gpl-2.0
| 5,227
|
[
"NEURON"
] |
c8cc5e3f1c5abfea19b5fd3e4579ae0610e63325f6b16d8eac8927b36a0f6e52
|
#! /usr/bin/env python
########################################################################
# File : dirac-admin-bdii-info
# Author : Aresh Vedaee
########################################################################
"""
Check info on BDII for a given CE or site
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOForGroup
def registerSwitches():
'''
Registers all switches that can be used while calling the script from the
command line interface.
'''
Script.registerSwitch("H:", "host=", "BDII host")
Script.registerSwitch("V:", "vo=", "vo")
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgfile] ... <info> <Site|CE>' % Script.scriptName,
'Arguments:',
' Site: Name of the Site (i.e. CERN-PROD)',
' CE: Name of the CE (i.e. cccreamceli05.in2p3.fr)',
' info: Accepted values (ce|ce-state|ce-cluster|ce-vo|site|site-se)']))
def parseSwitches():
'''
Parses the arguments passed by the user
'''
Script.parseCommandLine(ignoreErrors=True)
args = Script.getPositionalArgs()
if not len(args) == 2:
Script.showHelp()
params = {}
params['ce'] = None
params['site'] = None
params['host'] = None
params['vo'] = None
params['info'] = args[0]
ret = getProxyInfo(disableVOMS=True)
if ret['OK'] and 'group' in ret['Value']:
params['vo'] = getVOForGroup(ret['Value']['group'])
else:
Script.gLogger.error('Could not determine VO')
Script.showHelp()
if params['info'] in ['ce', 'ce-state', 'ce-cluster', 'ce-vo']:
params['ce'] = args[1]
elif params['info']in ['site', 'site-se']:
params['site'] = args[1]
else:
Script.gLogger.error('Wrong argument value')
Script.showHelp()
for unprocSw in Script.getUnprocessedSwitches():
if unprocSw[0] in ("H", "host"):
params['host'] = unprocSw[1]
if unprocSw[0] in ("V", "vo"):
params['vo'] = unprocSw[1]
return params
def getInfo(params):
'''
Retrieve information from BDII
'''
from DIRAC.Interfaces.API.DiracAdmin import DiracAdmin
diracAdmin = DiracAdmin()
if params['info'] == 'ce':
result = diracAdmin.getBDIICE(params['ce'], host=params['host'])
if params['info'] == 'ce-state':
result = diracAdmin.getBDIICEState(params['ce'], useVO=params['vo'], host=params['host'])
if params['info'] == 'ce-cluster':
result = diracAdmin.getBDIICluster(params['ce'], host=params['host'])
if params['info'] == 'ce-vo':
result = diracAdmin.getBDIICEVOView(params['ce'], useVO=params['vo'], host=params['host'])
if params['info'] == 'site':
result = diracAdmin.getBDIISite(params['site'], host=params['host'])
if params['info'] == 'site-se':
result = diracAdmin.getBDIISE(params['site'], useVO=params['vo'], host=params['host'])
if not result['OK']:
print result['Message']
DIRAC.exit(2)
return result
def showInfo(result, info):
'''
Display information
'''
elements = result['Value']
for element in elements:
if info == 'ce' or info == 'all':
print "CE: %s \n{" % element.get('GlueSubClusterName', 'Unknown')
if info == 'ce-state' or info == 'all':
print "CE: %s \n{" % element.get('GlueCEUniqueID', 'Unknown')
if info == 'ce-cluster' or info == 'all':
print "Cluster: %s \n{" % element.get('GlueClusterName', 'Unknown')
if info == 'ce-vo' or info == 'all':
print "CEVOView: %s \n{" % element.get('GlueChunkKey', 'Unknown')
if info == 'site' or info == 'all':
print "Site: %s \n{" % element.get('GlueSiteName', 'Unknown')
if info == 'site-se' or info == 'all':
print "SE: %s \n{" % element.get('GlueSEUniqueID', 'Unknown')
for item in element.iteritems():
print " %s: %s" % item
print "}"
# ...............................................................................
if __name__ == "__main__":
# Script initialization
registerSwitches()
# registerUsageMessage()
params = parseSwitches()
result = getInfo(params)
showInfo(result, params['info'])
DIRAC.exit(0)
################################################################################
# EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF
|
andresailer/DIRAC
|
ConfigurationSystem/scripts/dirac-admin-bdii-info.py
|
Python
|
gpl-3.0
| 4,570
|
[
"DIRAC"
] |
e162262e79dc1eef2751fba60e44afff66a4b9f915d50c2e9b031bf7baf1a017
|
#
# @file TestUnitDefinition.py
# @brief SBML UnitDefinition unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# src/sbml/test/TestUnitDefinition.c
# using the conversion program dev/utilities/translateTests/translateTests.pl.
# Any changes made here will be lost the next time the file is regenerated.
#
# -----------------------------------------------------------------------------
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
# Copyright 2005-2010 California Institute of Technology.
# Copyright 2002-2005 California Institute of Technology and
# Japan Science and Technology Corporation.
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation. A copy of the license agreement is provided
# in the file named "LICENSE.txt" included with this software distribution
# and also available online as http://sbml.org/software/libsbml/license.html
# -----------------------------------------------------------------------------
import sys
import unittest
import libsbml
class TestUnitDefinition(unittest.TestCase):
global UD
UD = None
def setUp(self):
self.UD = libsbml.UnitDefinition(2,4)
if (self.UD == None):
pass
pass
def tearDown(self):
_dummyList = [ self.UD ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_addUnit(self):
u = libsbml.Unit(2,4)
u.setKind(libsbml.UNIT_KIND_MOLE)
self.UD.addUnit(u)
self.assert_( self.UD.getNumUnits() == 1 )
_dummyList = [ u ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_create(self):
self.assert_( self.UD.getTypeCode() == libsbml.SBML_UNIT_DEFINITION )
self.assert_( self.UD.getMetaId() == "" )
self.assert_( self.UD.getNotes() == None )
self.assert_( self.UD.getAnnotation() == None )
self.assert_( self.UD.getId() == "" )
self.assert_( self.UD.getName() == "" )
self.assertEqual( False, self.UD.isSetId() )
self.assertEqual( False, self.UD.isSetName() )
self.assert_( self.UD.getNumUnits() == 0 )
pass
def test_UnitDefinition_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add( "http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2,1)
sbmlns.addNamespaces(xmlns)
object = libsbml.UnitDefinition(sbmlns)
self.assert_( object.getTypeCode() == libsbml.SBML_UNIT_DEFINITION )
self.assert_( object.getMetaId() == "" )
self.assert_( object.getNotes() == None )
self.assert_( object.getAnnotation() == None )
self.assert_( object.getLevel() == 2 )
self.assert_( object.getVersion() == 1 )
self.assert_( object.getNamespaces() != None )
self.assert_( object.getNamespaces().getLength() == 2 )
_dummyList = [ object ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_createWithName(self):
ud = libsbml.UnitDefinition(2,4)
ud.setName( "mmol_per_liter_per_sec")
self.assert_( ud.getTypeCode() == libsbml.SBML_UNIT_DEFINITION )
self.assert_( ud.getMetaId() == "" )
self.assert_( ud.getNotes() == None )
self.assert_( ud.getAnnotation() == None )
self.assert_( ud.getId() == "" )
self.assert_(( "mmol_per_liter_per_sec" == ud.getName() ))
self.assertEqual( True, ud.isSetName() )
self.assert_( ud.getNumUnits() == 0 )
_dummyList = [ ud ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_free_NULL(self):
_dummyList = [ None ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_getUnit(self):
mole = libsbml.Unit(2,4)
litre = libsbml.Unit(2,4)
second = libsbml.Unit(2,4)
mole.setKind(libsbml.UnitKind_forName("mole"))
litre.setKind(libsbml.UnitKind_forName("litre"))
second.setKind(libsbml.UnitKind_forName("second"))
mole.setScale(-3)
litre.setExponent(-1)
second.setExponent(-1)
self.UD.addUnit(mole)
self.UD.addUnit(litre)
self.UD.addUnit(second)
_dummyList = [ mole ]; _dummyList[:] = []; del _dummyList
_dummyList = [ litre ]; _dummyList[:] = []; del _dummyList
_dummyList = [ second ]; _dummyList[:] = []; del _dummyList
self.assert_( self.UD.getNumUnits() == 3 )
mole = self.UD.getUnit(0)
litre = self.UD.getUnit(1)
second = self.UD.getUnit(2)
self.assert_( mole.getKind() == libsbml.UNIT_KIND_MOLE )
self.assert_( litre.getKind() == libsbml.UNIT_KIND_LITRE )
self.assert_( second.getKind() == libsbml.UNIT_KIND_SECOND )
self.assert_( mole.getScale() == -3 )
self.assert_( litre.getExponent() == -1 )
self.assert_( second.getExponent() == -1 )
pass
def test_UnitDefinition_isVariantOfArea(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfArea() )
u.setKind(libsbml.UNIT_KIND_METRE)
u.setExponent(2)
self.assertEqual( True, self.UD.isVariantOfArea() )
u.setScale(-1)
self.assertEqual( True, self.UD.isVariantOfArea() )
u.setMultiplier(2)
self.assertEqual( True, self.UD.isVariantOfArea() )
u.setOffset(3)
self.assertEqual( True, self.UD.isVariantOfArea() )
u.setExponent(3)
self.assertEqual( False, self.UD.isVariantOfArea() )
u.setExponent(2)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfArea() )
pass
def test_UnitDefinition_isVariantOfLength(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfLength() )
u.setKind(libsbml.UNIT_KIND_METRE)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfLength() )
u.setScale(-1)
self.assertEqual( True, self.UD.isVariantOfLength() )
u.setMultiplier(2)
self.assertEqual( True, self.UD.isVariantOfLength() )
u.setOffset(3)
self.assertEqual( True, self.UD.isVariantOfLength() )
u.setExponent(2)
self.assertEqual( False, self.UD.isVariantOfLength() )
u.setExponent(1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfLength() )
pass
def test_UnitDefinition_isVariantOfSubstancePerTime_1(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
perTime = self.UD.createUnit()
perTime.setKind(libsbml.UnitKind_forName("second"))
perTime.setExponent(-1)
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfSubstancePerTime() )
u.setKind(libsbml.UNIT_KIND_MOLE)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setScale(-1)
perTime.setScale(-1)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setMultiplier(2)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setOffset(3)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setExponent(-3)
self.assertEqual( False, self.UD.isVariantOfSubstancePerTime() )
u.setExponent(1)
perTime.setExponent(-3)
self.assertEqual( False, self.UD.isVariantOfSubstancePerTime() )
perTime.setExponent(-1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
_dummyList = [ dim ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_isVariantOfSubstancePerTime_2(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
perTime = self.UD.createUnit()
perTime.setKind(libsbml.UnitKind_forName("second"))
perTime.setExponent(-1)
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfSubstancePerTime() )
u.setKind(libsbml.UNIT_KIND_ITEM)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setScale(-1)
perTime.setScale(-1)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setMultiplier(2)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setOffset(3)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
u.setExponent(-3)
self.assertEqual( False, self.UD.isVariantOfSubstancePerTime() )
u.setExponent(1)
perTime.setExponent(-3)
self.assertEqual( False, self.UD.isVariantOfSubstancePerTime() )
perTime.setExponent(-1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfSubstancePerTime() )
_dummyList = [ dim ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_isVariantOfSubstancePerTime_3(self):
ud = libsbml.UnitDefinition(2,2)
dim = libsbml.Unit(2,2)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
perTime = ud.createUnit()
perTime.setKind(libsbml.UnitKind_forName("second"))
perTime.setExponent(-1)
u = ud.createUnit()
self.assertEqual( False, ud.isVariantOfSubstancePerTime() )
u.setKind(libsbml.UNIT_KIND_GRAM)
u.setExponent(1)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setScale(-1)
perTime.setScale(-1)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setMultiplier(2)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setOffset(3)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setExponent(-3)
self.assertEqual( False, ud.isVariantOfSubstancePerTime() )
u.setExponent(1)
perTime.setExponent(-3)
self.assertEqual( False, ud.isVariantOfSubstancePerTime() )
perTime.setExponent(-1)
ud.addUnit(dim)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
_dummyList = [ ud ]; _dummyList[:] = []; del _dummyList
_dummyList = [ dim ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_isVariantOfSubstancePerTime_4(self):
ud = libsbml.UnitDefinition(2,2)
dim = ud.createUnit()
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
perTime = ud.createUnit()
perTime.setKind(libsbml.UnitKind_forName("second"))
perTime.setExponent(-1)
u = ud.createUnit()
self.assertEqual( False, ud.isVariantOfSubstancePerTime() )
u.setKind(libsbml.UNIT_KIND_KILOGRAM)
u.setExponent(1)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setScale(-1)
perTime.setScale(-1)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setMultiplier(2)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setOffset(3)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
u.setExponent(-3)
self.assertEqual( False, ud.isVariantOfSubstancePerTime() )
u.setExponent(1)
perTime.setExponent(-3)
self.assertEqual( False, ud.isVariantOfSubstancePerTime() )
perTime.setExponent(-1)
ud.addUnit(dim)
self.assertEqual( True, ud.isVariantOfSubstancePerTime() )
_dummyList = [ ud ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_isVariantOfSubstance_1(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfSubstance() )
u.setKind(libsbml.UNIT_KIND_MOLE)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setScale(-1)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setMultiplier(2)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setOffset(3)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setExponent(-3)
self.assertEqual( False, self.UD.isVariantOfSubstance() )
u.setExponent(1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
pass
def test_UnitDefinition_isVariantOfSubstance_2(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfSubstance() )
u.setKind(libsbml.UNIT_KIND_ITEM)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setScale(-1)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setMultiplier(2)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setOffset(3)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
u.setExponent(-2)
self.assertEqual( False, self.UD.isVariantOfSubstance() )
u.setExponent(1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfSubstance() )
pass
def test_UnitDefinition_isVariantOfTime(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfTime() )
u.setKind(libsbml.UNIT_KIND_SECOND)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfTime() )
u.setScale(-10)
self.assertEqual( True, self.UD.isVariantOfTime() )
u.setMultiplier(10)
self.assertEqual( True, self.UD.isVariantOfTime() )
u.setOffset(30)
self.assertEqual( True, self.UD.isVariantOfTime() )
u.setExponent(2)
self.assertEqual( False, self.UD.isVariantOfTime() )
u.setExponent(1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfTime() )
pass
def test_UnitDefinition_isVariantOfVolume_1(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfVolume() )
u.setKind(libsbml.UNIT_KIND_LITRE)
u.setExponent(1)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setScale(100)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setMultiplier(5)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setOffset(-5)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setExponent(-1)
self.assertEqual( False, self.UD.isVariantOfVolume() )
u.setExponent(1)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfVolume() )
pass
def test_UnitDefinition_isVariantOfVolume_2(self):
dim = libsbml.Unit(2,4)
dim.setKind(libsbml.UnitKind_forName("dimensionless"))
u = self.UD.createUnit()
self.assertEqual( False, self.UD.isVariantOfVolume() )
u.setKind(libsbml.UNIT_KIND_METRE)
u.setExponent(3)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setScale(100)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setMultiplier(5)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setOffset(-5)
self.assertEqual( True, self.UD.isVariantOfVolume() )
u.setExponent(2)
self.assertEqual( False, self.UD.isVariantOfVolume() )
u.setExponent(3)
self.UD.addUnit(dim)
self.assertEqual( True, self.UD.isVariantOfVolume() )
pass
def test_UnitDefinition_printUnits(self):
ud = libsbml.UnitDefinition(2,4)
ud.setId( "mmls")
perTime = ud.createUnit()
perTime.setKind(libsbml.UnitKind_forName("second"))
perTime.setExponent(-1)
ud_str = libsbml.UnitDefinition.printUnits(ud,False)
self.assert_(( "second (exponent = -1, multiplier = 1, scale = 0)" == ud_str ))
ud_str1 = libsbml.UnitDefinition.printUnits(ud,True)
self.assert_(( "(1 second)^-1" == ud_str1 ))
ud1 = libsbml.UnitDefinition(2,4)
ud1.setId( "mmls")
u = ud1.createUnit()
u.setKind(libsbml.UNIT_KIND_KILOGRAM)
u.setExponent(1)
u.setScale(2)
u.setMultiplier(3.0)
ud_str2 = libsbml.UnitDefinition.printUnits(ud1,False)
self.assert_(( "kilogram (exponent = 1, multiplier = 3, scale = 2)" == ud_str2 ))
ud_str3 = libsbml.UnitDefinition.printUnits(ud1,True)
self.assert_(( "(300 kilogram)^1" == ud_str3 ))
pass
def test_UnitDefinition_removeUnit(self):
o1 = self.UD.createUnit()
o2 = self.UD.createUnit()
o3 = self.UD.createUnit()
self.assert_( self.UD.removeUnit(0) == o1 )
self.assert_( self.UD.getNumUnits() == 2 )
self.assert_( self.UD.removeUnit(0) == o2 )
self.assert_( self.UD.getNumUnits() == 1 )
self.assert_( self.UD.removeUnit(0) == o3 )
self.assert_( self.UD.getNumUnits() == 0 )
_dummyList = [ o1 ]; _dummyList[:] = []; del _dummyList
_dummyList = [ o2 ]; _dummyList[:] = []; del _dummyList
_dummyList = [ o3 ]; _dummyList[:] = []; del _dummyList
pass
def test_UnitDefinition_setId(self):
id = "mmls";
self.UD.setId(id)
self.assert_(( id == self.UD.getId() ))
self.assertEqual( True, self.UD.isSetId() )
if (self.UD.getId() == id):
pass
self.UD.setId(self.UD.getId())
self.assert_(( id == self.UD.getId() ))
self.UD.setId("")
self.assertEqual( False, self.UD.isSetId() )
if (self.UD.getId() != None):
pass
pass
def test_UnitDefinition_setName(self):
name = "mmol_per_liter_per_sec";
self.UD.setName(name)
self.assert_(( name == self.UD.getName() ))
self.assertEqual( True, self.UD.isSetName() )
if (self.UD.getName() == name):
pass
self.UD.setName(self.UD.getName())
self.assert_(( name == self.UD.getName() ))
self.UD.setName("")
self.assertEqual( False, self.UD.isSetName() )
if (self.UD.getName() != None):
pass
pass
def suite():
suite = unittest.TestSuite()
suite.addTest(unittest.makeSuite(TestUnitDefinition))
return suite
if __name__ == "__main__":
if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
sys.exit(0)
else:
sys.exit(1)
|
alexholehouse/SBMLIntegrator
|
libsbml-5.0.0/src/bindings/python/test/sbml/TestUnitDefinition.py
|
Python
|
gpl-3.0
| 18,004
|
[
"VisIt"
] |
99fb193b9b1a0a5bc8c69c0ebdd8a823699385960bfb886de3d0419faef11cff
|
"""
Image processing routines
Most of these are specific to PyVoyager
"""
import os
import os.path
import scipy.ndimage as ndimage # n-dimensional images - for blob detection
import numpy as np
import cv2
import math
import random
import PIL
from PIL import Image
from PIL import ImageFont
from PIL import ImageDraw
import config
import lib
import log
import ransac
def cropImageFile(infile, outfile, tx=0, ty=0, scale=1.0):
"crop/zoom in on image file - tx,ty are location of top-left corner in existing image"
im = cv2.imread(infile, cv2.IMREAD_GRAYSCALE)
im = cropImage(im, tx, ty, scale)
cv2.imwrite(outfile, im)
def cropImage(im, tx=0, ty=0, scale=1.0):
"crop/zoom in on image - tx,ty are location of top-left corner in existing image"
im = shiftImage(im, tx,ty)
M = np.float32([[scale,0,0],[0,scale,0]])
# note: INTER_LINEAR (default) or INTER_CUBIC (slow) is preferred for zooming
# see http://docs.opencv.org/trunk/da/d6e/tutorial_py_geometric_transformations.html
# note: don't need to specify size/shape if not changing it - just pass None
im = cv2.warpAffine(im, M, None, flags=cv2.INTER_CUBIC)
return im
class Page:
"""
wrapper around PIL text writing routines
eg
page = Page()
page.vtab(5)
page.println(title, color=200, center=True)
page.save(filepath)
"""
def __init__(self, size=800):
"create a page to write on"
self.size = size
self.imgsize = [size,size] #.param - will be 1000x1000
self.bgcolor = (0,0,0)
self.img = Image.new("RGBA", self.imgsize, self.bgcolor)
self.draw = ImageDraw.Draw(self.img)
self.pos = [0,0]
self.fontpath = config.titleFont
self.fontsize = config.titleFontsize
self.setfont(self.fontpath, self.fontsize)
def htab(self, col):
"horizontal tab"
self.pos[0] = col * self.charWidth
def vtab(self, row):
"vertical tab"
self.pos[1] = row * self.charHeight
def setfont(self, fontpath=None, fontsize=None):
"change font/size"
fontpath = fontpath or self.fontpath
fontsize = fontsize or self.fontsize
self.font = ImageFont.truetype(fontpath, fontsize)
self.charWidth, self.charHeight = self.font.getsize("M")
self.charHeight *= 1.3 # fudge factor
def println(self, s, color=160, center=False):
"print a line or sequence of lines"
lines = s.split('\n')
fg = (color,color,color)
for line in lines:
w,h = self.font.getsize(line)
if center:
self.pos[0] = (self.size - w) / 2
self.draw.text(self.pos, line, fg, font=self.font)
# self.pos[1] = self.pos[1] + h*1.25
self.pos[1] = self.pos[1] + self.charHeight
def save(self, filepath):
"save page to a file"
self.img.save(filepath)
def thresholdImage(im):
"get adaptive threshold of image"
im = cv2.adaptiveThreshold(im, maxValue=255,
adaptiveMethod=cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
thresholdType=cv2.THRESH_BINARY_INV,
blockSize=3,
C=10)
return im
def getImageAlignment(im0, im1, dx=0, dy=0):
"""
Get alignment between images using different methods available.
Returns dx,dy,ok
Returns 0,0,False if no alignment found
"""
dx,dy,ok = getImageAlignmentORB(im0, im1)
if not ok:
dx,dy,ok = getImageAlignmentECC(im0, im1, dx=dx, dy=dy) # initialize with dx,dy
# dx,dy,ok = getImageAlignmentDiff(im0, im1)
return dx,dy,ok
def getImageAlignmentDiff(im0, im1):
"""
get image alignment by minimizing the sum of differences between images
#. this doesn't work very well yet
"""
# lores image size
# sz = 100
sz = 200
# sz = 40
# tilesize = 40
tilesize = 25
# tilesize = 20
# tilesize = 10
# get lores versions
im0sm = resizeImage(im0,sz,sz)
im1sm = resizeImage(im1,sz,sz)
show(im0sm)
show(im1sm)
dx=dy=0
imax=jmax=sz-tilesize
istep=1
# get tile from im1
nsteps = sz/tilesize
dxsum=dysum=0
for tilex in range(0,sz-tilesize,tilesize):
for tiley in range(0,sz-tilesize,tilesize):
tile = im1sm[tiley:tiley+tilesize, tilex:tilex+tilesize]
# libimg.show(tile)
# use opencv template matching routine
# for examples of methods see
# http://docs.opencv.org/3.1.0/d4/dc6/tutorial_py_template_matching.html
# method = cv2.TM_SQDIFF
# method = cv2.TM_SQDIFF_NORMED
# method = cv2.TM_CCOEFF
# method = cv2.TM_CCOEFF_NORMED
# method = cv2.TM_CCORR
method = cv2.TM_CCORR_NORMED
res = cv2.matchTemplate(im0sm,tile,method)
# res = cv2.matchTemplate(im1sm,tile,method) # sanity check
min_val, max_val, min_loc, max_loc = cv2.minMaxLoc(res)
# top_left = min_loc
if method in [cv2.TM_SQDIFF, cv2.TM_SQDIFF_NORMED]:
top_left = min_loc
else:
top_left = max_loc
# w=h=tilesize
# bottom_right = (top_left[0] + w, top_left[1] + h)
# cv2.rectangle(res,top_left, bottom_right, 255, 1)
# show(res)
dx = top_left[0]-tilex
dy = top_left[1]-tiley
dxsum+=dx
dysum+=dy
dx = dxsum/nsteps/nsteps; dy = dysum/nsteps/nsteps
dx *= 800/sz; dy *= 800/sz
# dx,dy=dy,dx
dx=-dx;dy=-dy
# print dx,dy
im1shifted = shiftImage(im1, dx,dy)
show(im1shifted)
return dx,dy,True
def getImageAlignmentORB(im0, im1):
"""
Get alignment between images using ORB feature alignment.
Returns dx,dy,alignmentOk
If unable to align images returns 0,0,False
"""
npoints = 500 # default
# npoints = 100
sz = 800
# sz = 400
# sz = 200
# sz = 100
# magnitude = True
magnitude = False # best
sharpen = False # best
# sharpen = True
contrast = True # best (using equalize hist)
# contrast = False
# neighborhood = 121
# neighborhood = 51
neighborhood = 31 # default and best
# neighborhood = 21
# neighborhood = 15
# neighborhood = 13
# neighborhood = 11
# neighborhood = 9
# neighborhood = 7
# fastThreshold = 20 # default
fastThreshold = 10 # best
# fastThreshold = 5
# fastThreshold = 1
# fastThreshold = 0
# knnMatching = True
knnMatching = False # best
crossCheck = True # best
# crossCheck = False # need False so knnMatch works - why?
# keepMatches = 50
# keepMatches = 40
# keepMatches = 30
# keepMatches = 20
keepMatches = 10 # best
# keepMatches = 5
transform = 'translate' # best
# transform = 'affine'
# transform = 'homography'
# shrink image
if sz!=800:
im0 = resizeImage(im0,sz,sz)
im1 = resizeImage(im1,sz,sz)
if magnitude:
im0 = getGradientMagnitude(im0)
im1 = getGradientMagnitude(im1)
if sharpen:
im0 = sharpenImage(im0)
im1 = sharpenImage(im1)
if contrast:
# three types of contrast enhancement - equalizeHist works best
im0 = cv2.equalizeHist(im0)
im1 = cv2.equalizeHist(im1)
# ---
# clahe = cv2.createCLAHE(clipLimit=4.0, tileGridSize=(8,8))
# im0 = clahe.apply(im0)
# im1 = clahe.apply(im1)
# ---
# maxIntensity = 255.0
# phi = 1
# theta = 1
# expt = 2
# x = np.arange(maxIntensity)
# im0 = (maxIntensity/phi)*(im0/(maxIntensity/theta))**expt
# im1 = (maxIntensity/phi)*(im1/(maxIntensity/theta))**expt
# im0 = np.array(im0,dtype=np.uint8)
# im1 = np.array(im1,dtype=np.uint8)
# bug patch - see https://github.com/opencv/opencv/issues/6081
cv2.ocl.setUseOpenCL(False)
# Initiate ORB detector
# ORB is basically a fusion of FAST keypoint detector and BRIEF descriptor
# with many modifications to enhance the performance. First it use FAST to
# find keypoints, then apply Harris corner measure to find top N points
# among them. It also use pyramid to produce multiscale-features.
# ORB (oriented BRIEF) keypoint detector and descriptor extractor.
# described in [125] . The algorithm uses FAST in pyramids to detect stable
# keypoints, selects the strongest features using FAST or Harris response,
# finds their orientation using first-order moments and computes the
# descriptors using BRIEF (where the coordinates of random point pairs (or
# k-tuples) are rotated according to the measured orientation).
# defaults:
# create (int nfeatures=500, float scaleFactor=1.2f, int nlevels=8,
# int edgeThreshold=31, int firstLevel=0, int WTA_K=2,
# int scoreType=ORB::HARRIS_SCORE, int patchSize=31, int fastThreshold=20)
# scaleFactor is for scaling the images down (or the detector patch
# up) between octaves (or levels). for less calculations, use a
# scaling of 1.5f and 4 levels.
# orb = cv2.ORB_create()
orb = cv2.ORB_create(npoints, edgeThreshold=neighborhood,
patchSize=neighborhood, fastThreshold=fastThreshold)
# find the keypoints and their descriptors
# kp0, des0 = orb.detectAndCompute(im0,None)
# kp1, des1 = orb.detectAndCompute(im1,None)
# detect keypoints
kp0 = orb.detect(im0,None) # None is a mask you can pass
kp1 = orb.detect(im1,None)
# compute descriptors for keypoints
kp0, des0 = orb.compute(im0,kp0)
kp1, des1 = orb.compute(im1,kp1)
# exit if no keypoints or descriptors found
if des0 is None or des1 is None:
print 'des0 or des1 is none - ie no keypoints found'
return 0,0,False
# out = cv2.drawKeypoints(im0,kp0,None)
# show(out)
# create brute force matcher
# see http://docs.opencv.org/3.0-beta/doc/py_tutorials/py_feature2d/py_matcher/py_matcher.html
# need to use NORM_HAMMING since ORB is a binary feature
#. what exactly does crossCheck do?
matcher = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=crossCheck)
if not knnMatching:
# match descriptors and sort them in order of distance
matches = matcher.match(des0,des1)
matches = sorted(matches, key = lambda x:x.distance)
good = matches[:keepMatches]
else:
# use K nearest neighbor matching
matches = matcher.knnMatch(des0,des1,k=2)
# get all the good matches as per Lowe's ratio test
good = [m[0] for m in matches if len(m) == 2 and m[0].distance < m[1].distance * 0.75]
# print 'good matches',len(good)
# draw good matches
# shows images side by side with colored lines between matched points
#........... make debug flag to save this image to a debug folder? useful to look through them
# out = cv2.drawMatches(im0,kp0,im1,kp1,good,None,
# flags=cv2.DRAW_MATCHES_FLAGS_DRAW_RICH_KEYPOINTS)
# show(out)
# find transformation matrix
if transform=='translate':
# simple translation (x,y shift)
# get simple translation model - includes ransac outlier elimination
pts0 = [kp0[m.queryIdx].pt for m in good]
pts1 = [kp1[m.trainIdx].pt for m in good]
data = zip(pts0,pts1)
dx, dy, modelOk = ransac.getRansacModel(data)
if not modelOk:
print 'no ransac model found'
return 0,0,False
# imx = cv2.warpAffine(im1, M, (cols,rows),
# flags = cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
imx = shiftImage(im1, dx, dy)
# show(imx)
blank = np.zeros((sz,sz),np.uint8)
# imy = cv2.merge((blank, im0, imx))
imy = cv2.merge((im0, blank, imx)) # base image is blue, moved is red
# show(imy)
elif transform=='affine':
# Affine transformation (shift, rotation, scaling, shear)
# note: M might include a bit of rotation, but we'll just ignore that
# this includes RANSAC to eliminate outliers - see
# https://github.com/opencv/opencv/blob/master/modules/video/src/lkpyramid.cpp
pts0 = np.float32([ kp0[m.queryIdx].pt for m in good ]).reshape(-1,1,2)
pts1 = np.float32([ kp1[m.trainIdx].pt for m in good ]).reshape(-1,1,2)
M = cv2.estimateRigidTransform(pts0, pts1, False)
if M is None:
print 'M is none - no good solution found'
return 0,0,False
# print M
# eg
# [[ 1.00273314e+00 2.62991563e-03 -1.53541381e+02]
# [ -2.62991563e-03 1.00273314e+00 -1.77198771e+01]]
# show images
# # just want pure translation
# M[0][0]=1
# M[0][1]=0
# M[1][0]=0
# M[1][1]=1
# # note order of cols, rows -
# rows, cols = im1.shape[:2]
# imx = cv2.warpAffine(im1, M, (cols,rows),
# flags = cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
# show(imx)
# blank = np.zeros((sz,sz),np.uint8)
# imy = cv2.merge((blank, im0, imx))
# show(imy)
dx = M[0][2]
dy = M[1][2]
elif transform=='homography':
# Homography transform (shift, rotate, scale, skew, tilt)
# initialize arrays of keypoint coordinates
pts0list = []
pts1list = []
for m in good:
# get the matching keypoints for each of the images
im0idx = m.queryIdx
im1idx = m.trainIdx
# get the coordinates
(x0,y0) = kp0[im0idx].pt
(x1,y1) = kp1[im1idx].pt
# append to each list
pts0list.append((x0, y0))
pts1list.append((x1, y1))
pts0 = np.array(pts0list)
pts1 = np.array(pts1list)
# see http://docs.opencv.org/2.4/modules/calib3d/doc/
# camera_calibration_and_3d_reconstruction.html#findhomography
H, status = cv2.findHomography(pts0, pts1, cv2.RANSAC, 5.0) #. 5.0=?
if H is None:
print 'H is none - no good solution found - %d good matches' % len(good)
return 0,0,False
print H
# imx = shiftImage(im1, dx, dy)
# # show(imx)
# blank = np.zeros((sz,sz),np.uint8)
# imy = cv2.merge((blank, im0, imx))
# # show(imy)
dx = H[0][2]
dy = H[1][2]
# return results
if sz!=800: dx*=800/sz;dy*=800/sz #.params
alignmentOk = True
return dx,dy,alignmentOk
def sharpenImage(im):
"sharpen image with a simple 2d kernel"
kernel = np.array([[0,-1,0], [-1,5,-1], [0,-1,0]])
# kernel = np.array([[-1,-1,-1], [-1,9,-1], [-1,-1,-1]]) # a bit too sharp, even for clouds
# kernel = np.array([[-1,-1,-1,-1,-1],
# [-1,2,2,2,-1],
# [-1,2,8,2,-1],
# [-1,2,2,2,-1],
# [-1,-1,-1,-1,-1]]) / 8.0
# kernel = np.array([[1,1,1], [1,-7,1], [1,1,1]]) # blur
im = cv2.filter2D(im, -1, kernel)
return im
def imwrite(outfile, im):
"""
like cv2.imwrite but on error will try to create the outfile's folder also.
useful in some cases where not known if folder exists or not.
"""
ok = cv2.imwrite(outfile, im)
if not ok:
folder = os.path.dirname(outfile)
lib.mkdir(folder)
ok = cv2.imwrite(outfile, im)
return ok
def inpaintImage(infile, priorfile, outfile, targetRadius):
"""
fill in regions of black or white inside targetRadius in infile using pixels from priorfile.
assumes both files are centered on the target.
targetRadius is the expected size of the target.
"""
debug = False
# read image and prior image
im = cv2.imread(infile, 0) #.param
imPrior = cv2.imread(priorfile, 0) #.param
if debug: show(im)
if debug: show(imPrior)
# get mask for target radius
maskTarget = np.zeros(im.shape[:2], np.uint8)
maskTarget = cv2.circle(maskTarget, (399,399), targetRadius, 255, -1) # -1=filled #.params
if debug: show(maskTarget)
# get mask where image is black
maskBlack = np.array(255 * (im<=4), np.uint8) #.param
if debug: show(maskBlack)
# get mask where image is white
maskWhite = np.array(255 * (im>=255), np.uint8) #.param
if debug: show(maskWhite)
# combine the masks
maskEmpty = maskBlack | maskWhite
if debug: show(maskEmpty)
# merge with target mask
maskPaint = maskTarget & maskEmpty
if debug: show(maskPaint)
# pull pixels from imPrior where mask is
imOut = (im & (255-maskPaint)) + (imPrior & maskPaint)
if debug: show(imOut)
# cv2.imwrite(outfile, imOut)
imwrite(outfile, imOut)
def getGradientMagnitude(im):
"Get magnitude of gradient for given image using simple kernel"
ddepth = cv2.CV_32F
kernel = np.zeros((1,3))
kernel[0][0]=-1
kernel[0][1]=0
kernel[0][2]=1
dx = cv2.filter2D(im, ddepth, kernel)
dxabs = cv2.convertScaleAbs(dx)
kernel = np.zeros((3,1))
kernel[0][0]=-1
kernel[1][0]=0
kernel[2][0]=1
dy = cv2.filter2D(im, ddepth, kernel)
dyabs = cv2.convertScaleAbs(dy)
mag = cv2.addWeighted(dxabs, 0.5, dyabs, 0.5, 0)
return mag
def getGradientMagnitudeSobel(im):
"""
Calculate the x and y gradients using Sobel operator.
Sobel includes Gaussian filtering, so may not be ideal for detecting noise.
"""
# ddepth = cv2.CV_32F
# dx = cv2.Sobel(im, ddepth, 1, 0)
# dy = cv2.Sobel(im, ddepth, 0, 1)
#. wouldn't ksize=3 just make it same as previous fn (with [-1 0 1] kernels)?
dx = cv2.Sobel(im, ddepth, 1, 0, ksize=3)
dy = cv2.Sobel(im, ddepth, 0, 1, ksize=3)
# Combine the two gradients
mag = cv2.addWeighted(np.absolute(dx), 0.5, np.absolute(dy), 0.5, 0)
return mag
def annotateImageFile(infile, outfile, imageId, time, distance, note):
"""
Overlay some information on given input file and write to outfile
"""
font = ImageFont.truetype(config.annotationsFont, config.annotationsFontsize)
fgcolor = (200,200,200)
w,h = font.getsize('M')
img = Image.open(infile)
if img!='RGB': img = img.convert('RGB') # else some images cause TypeError on draw text
draw = ImageDraw.Draw(img)
pos = (50,625)
s = imageId
draw.text(pos, s, fgcolor, font=font)
pos = (pos[0],pos[1]+int(h*1.5))
s = time
draw.text(pos, s, fgcolor, font=font)
pos = (pos[0],pos[1]+int(h*1.5))
s = distance
draw.text(pos, s, fgcolor, font=font)
pos = (pos[0],pos[1]+int(h*1.5))
s = note
draw.text(pos, s, fgcolor, font=font)
pos = (pos[0],pos[1]+int(h*1.5))
img.save(outfile)
def denoiseImageFile(infile, outfile):
"""
attempt to remove noise from the given image file and save to outfile
"""
im = cv2.imread(infile, 0) #.param
# blank out bottom 3 pixels
im[-3:,:] = 0
# blank out right 3 pixels
im[:,-3:] = 0
# nowork - blurs some nice images - jupiter, triton ice
# remove salt and pepper noise, and thin lines
# im = cv2.medianBlur(im, 5)
# nowork - inpainting doesn't look very good
# remove larger blocks of noise by inpainting
# first detect regions with lots of variation
# mag = getGradientMagnitude(im)
# mask = cv2.adaptiveThreshold(im, maxValue=255,
# adaptiveMethod=cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
# thresholdType=cv2.THRESH_BINARY_INV,
# blockSize=3,
# C=8)
# # ret, mask = cv2.threshold(im, 200, 255, cv2.THRESH_BINARY) # nope
# # kernel = np.ones((5,1),np.uint8)
# kernel = np.ones((10,1),np.uint8)
# mask = cv2.dilate(mask, kernel, iterations = 1)
# # im = cv2.inpaint(im, mask, inpaintRadius=3, flags=cv2.INPAINT_TELEA)
# im = cv2.inpaint(im, mask, inpaintRadius=5, flags=cv2.INPAINT_TELEA)
# black out large blocks of noise
# # detect contours of noisy areas
# mask = cv2.adaptiveThreshold(im, maxValue=255,
# adaptiveMethod=cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
# thresholdType=cv2.THRESH_BINARY_INV,
# blockSize=3,
# C=11)
# kernel = np.ones((2,21), np.uint8)
# mask = cv2.morphologyEx(mask, cv2.MORPH_CLOSE, kernel) # dilate then erode
# # find contours and bounding boxes, pick out rectangular ones and black whole rectangle out
# im2, contours, hierarchy = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
# for contour in contours:
# x,y,w,h = cv2.boundingRect(contour)
# if w>100 and w>h*3:
# cv2.rectangle(im, (x,y), (x+w,y+h), 0, -1) # filled black rectangle
#
mask = getGradientMagnitude(im)
mask = cv2.adaptiveThreshold(mask, maxValue=255,
adaptiveMethod=cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
thresholdType=cv2.THRESH_BINARY_INV,
blockSize=3,
# C=25)
C=30)
# this extracts any long horizontal segments
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (120,1));
mask = cv2.dilate(mask, kernel)
# this __
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (20,5));
mask = cv2.dilate(mask, kernel)
mask = cv2.erode(mask, kernel)
im = im & (255-mask)
# try removing noise near sharp edges (median blur)
# the larger C is, the less noise will be removed
mask = cv2.adaptiveThreshold(im, maxValue=255,
adaptiveMethod=cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
thresholdType=cv2.THRESH_BINARY_INV,
blockSize=3,
# C=2) # ends up blurring triton
# C=5) # leaves too much noise
C=4) # good compromise
kernel = np.ones((5,5), np.uint8) # expand edges horizontally
mask = cv2.dilate(mask, kernel, iterations = 1) # expand edge mask
mask = cv2.medianBlur(mask, 5) # remove dots from mask
imblurred = cv2.medianBlur(im, 5) # remove noise from image
im = im + ((imblurred - im) & mask) # combine image with blurred version
# nowork
# # fill in single pixel horizontal lines
# # first identify horizontal segments - then get avg of above and below pixels
# linesToFill = []
# im2 = im
# for j in xrange(0,800):
# rowMiddle = im[j,:]
# # rowAbove = im[j-1,:] if j>0 else np.zeros(800,np.uint8)
# # rowBelow = im[j+1,:] if j<799 else np.zeros(800,np.uint8)
# rowAbove = im2[j-1,:] if j>0 else np.zeros(800,np.uint8)
# rowBelow = im2[j+1,:] if j<799 else np.zeros(800,np.uint8)
# maxlen = 0
# seglen = 0
# for i in xrange(0,800):
# above = rowAbove[i]
# middle = rowMiddle[i]
# below = rowBelow[i]
# # d1 = middle-above
# # d2 = middle-below
# # if (middle>above and middle>below) or (middle<above and middle<below):
# # eps=30
# # above = above + eps
# # below = below + eps
# if (middle>above and middle>below):
# seglen += 1
# if seglen>maxlen:
# maxlen = seglen
# else:
# seglen = 0
# # if maxlen > 20: #.param
# if maxlen > 30: #.param
# linesToFill.append(j)
# for line in linesToFill:
# rowAbove = im[line-1,:] if line>0 else np.zeros(800,np.uint8)
# rowBelow = im[line+1,:] if line<799 else np.zeros(800,np.uint8)
# # im[line,:] = 0
# im[line,:] = (rowAbove+rowBelow)/2
# cv2.imwrite(outfile, im)
imwrite(outfile, im)
def resizeImage(im, w, h):
"Resize image, keeping aspect ratio, filling in gaps with black, return new image."
oldH, oldW = im.shape[:2]
aspectRatio = float(oldW) / float(oldH)
if aspectRatio > 1: # width>height
newW = w
newH = int(newW / aspectRatio)
else:
newH = h
newW = int(newH * aspectRatio)
# scale the image
# http://docs.opencv.org/trunk/da/d6e/tutorial_py_geometric_transformations.html
zooming = (newW<w) or (newH<h)
if zooming:
# INTER_LINEAR and INTER_CUBIC (slow) is preferred for zooming
# note: this takes w,h not h,w!
# im = cv2.resize(im, (newW,newH), interpolation=cv2.INTER_AREA)
im = cv2.resize(im, (newW,newH), interpolation=cv2.INTER_CUBIC)
else:
# INTER_AREA is preferred for shrinking
im = cv2.resize(im, (newW,newH), interpolation=cv2.INTER_AREA)
# add the new image to a blank canvas
canvas = np.zeros(im.shape, np.uint8)
x = int((w-newW)/2)
y = int((h-newH)/2)
canvas[y:y+newH, x:x+newW] = im
return canvas
def getImageAlignmentECC(imFixed, im, dx=0, dy=0):
"""
Get alignment between images using ECC maximization algorithm.
Returns dx,dy,alignmentOk
If unable to align images returns 0,0,False
"""
mode = cv2.MOTION_TRANSLATION
M = np.eye(2, 3, dtype=np.float32) #. add paramnames
# can pass in initial guess
M[0][2] = dx
M[1][2] = dy
criteria = (cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT,
config.stabilizeECCIterations, config.stabilizeECCTerminationEpsilon)
# run the ECC algorithm
# throws an error if doesn't converge, so catch it
try:
cc, M = cv2.findTransformECC(imFixed, im, M, mode, criteria)
except Exception, e:
print 'exception', e
# if can't find solution, images aren't close enough in similarity
dx = 0
dy = 0
alignmentOk = False
else:
# eg
# print M
# [[ 1. 0. 1.37005 ]
# [ 0. 1. 0.485788]]
dx = M[0][2]
dy = M[1][2]
dx = int(round(dx))
dy = int(round(dy))
alignmentOk = True
return dx,dy,alignmentOk
def centerAndStabilizeImageFile(infile, targetRadius):
"""
Center the given image file on a target and return x,y.
Stabilize infile against disc of radius targetRadius and write to outfile.
Returns dx,dy,stabilizationOk
targetRadius is the expected radius, in pixels
"""
im = cv2.imread(infile, cv2.IMREAD_GRAYSCALE)
# find the bounding box of biggest object
# either a blob or a circle
boundingBox = findBoundingBox(im, targetRadius)
# center the image on the target
im = centerImage(im, boundingBox)
x = int((boundingBox[0] + boundingBox[2])/2)
y = int((boundingBox[1] + boundingBox[3])/2)
# this is pretty approximate when it's just a blob
# foundRadius = int((boundingBox[2]-x + boundingBox[3]-y)/2)
# return x, y, foundRadius
# get fixed image of filled target disc
imFixed = np.zeros((800,800), np.uint8) #.params
cv2.circle(imFixed, (399,399), targetRadius, 255, -1) # -1=filled #.params
# align the image to the target disc
dx, dy, alignmentOk = getImageAlignmentECC(imFixed, im)
if alignmentOk:
im = shiftImage(im, dx, dy)
x += dx
y += dy
return x,y
def stabilizeImageFile(infile, outfile, targetRadius):
"""
Stabilize infile against disc of radius targetRadius and write to outfile.
Returns dx,dy,stabilizationOk
targetRadius is the expected radius, in pixels
"""
# get fixed image of filled target disc
imFixed = np.zeros((800,800), np.uint8) #.params
cv2.circle(imFixed, (399,399), targetRadius, 255, -1) # -1=filled #.params
# get input file
im = cv2.imread(infile, cv2.IMREAD_GRAYSCALE)
# align the image to the target disc
# dx, dy, alignmentOk = getImageAlignment(imFixed, im)
dx, dy, alignmentOk = getImageAlignmentECC(imFixed, im)
if alignmentOk:
im = shiftImage(im, dx, dy)
# this doesn't work as precisely (why?), and it's about same speed, so just use warp
# im = translateImage(im, dx, dy)
#. bug - these flags kept getting set to True, but where?
# print config.drawCrosshairs, config.drawTarget
# if config.drawCrosshairs:
# drawCrosshairs(im)
# if config.drawTarget:
# im = gray2rgb(im)
# circle = (399,399,targetRadius) #.params
# drawCircle(im, circle, color = (0,255,255)) # yellow circle
if outfile:
imwrite(outfile, im)
return dx,dy,alignmentOk
def translateImage(im, dx, dy):
"translate an image by the given delta x,y, keeping same image size"
#. eliminate this
# see also shiftImage, which works better
cx = int(im.shape[1]/2)
cy = int(im.shape[0]/2)
x = int(cx - dx)
y = int(cy - dy)
boundingBox = [x,y,x,y]
im = centerImage(im, boundingBox)
return im
def centerImageFileAt(infile, outfile, x, y):
"""
Center the given image file at the given x,y and save it to outfile.
"""
im = cv2.imread(infile, cv2.IMREAD_GRAYSCALE)
# center the image on the target
boundingBox = [x,y,x,y]
im = centerImage(im, boundingBox)
if config.drawCrosshairs:
drawCrosshairs(im)
imwrite(outfile, im)
def centerImageFile(infile, outfile=None, targetRadius=None):
"""
Center the given image file on a target and save it to outfile, if given.
Returns x,y,foundRadius
"""
im = cv2.imread(infile, cv2.IMREAD_GRAYSCALE)
# find the bounding box of biggest object
# either a blob or a circle
boundingBox = findBoundingBox(im, targetRadius)
# center the image on the target
im = centerImage(im, boundingBox)
if outfile:
imwrite(outfile, im)
x = int((boundingBox[0] + boundingBox[2])/2)
y = int((boundingBox[1] + boundingBox[3])/2)
# this is pretty approximate when it's just a blob
foundRadius = int((boundingBox[2]-x + boundingBox[3]-y)/2)
return x, y, foundRadius
def drawCrosshairs(im):
"draw crosshairs on given image"
color = 64
xmax = im.shape[1]
ymax = im.shape[0]
cx = int(xmax/2)
cy = int(ymax/2)
im[cy, 0:xmax-1] = color
im[0:ymax-1, cx] = color
def img2png(srcdir, filespec, destdir):
"Convert all IMG files matching filespec in srcdir to PNG files in destdir"
# first convert img's to png's, then move them to the dest dir
savedir = os.getcwd()
os.chdir(srcdir)
# eg "img2png *CALIB.img -fnamefilter > nul"
cmd = "img2png " + filespec + " " + config.img2pngOptions + " > nul"
os.system(cmd)
# now move the png files to destdir
#. use os.rename - should be faster
# (srcdir is relative to the python program so need to switch back to that dir)
os.chdir(savedir)
# cmd = "mv " + srcdir +"*.png " + destdir + " > nul" # nowork on windows due to backslashes
cmd = "move " + srcdir +"\\*.png " + destdir + " > nul"
os.system(cmd)
# def stretchHistogram(im, nHotPixels=100):
def stretchHistogram16to8bit(im, maxvalue=None):
"""
stretch the histogram of the given 16bit image and return it as an 8bit image.
hot pixels are set at 32767, but hot noise can exist in an image also.
can pass maxvalue
"""
# get histogram
# see http://docs.opencv.org/3.1.0/d1/db7/tutorial_py_histogram_begins.html
# eg hist = cv2.calcHist([im],[0],mask,[256],[0,256])
images = [im]
channels = [0]
mask = None # lets you filter to part of an image
histSize = [256] # number of bins
# ranges = [0, 256] # range of intensity values
ranges = [0, 32768] # range of intensity values
hist = cv2.calcHist(images, channels, mask, histSize, ranges)
# print [int(x) for x in hist]
# # ignore top n pixels
# # start at top, get cumulative sum downwards until reach certain amount of pixels
# npixels = im.shape[0] * im.shape[1]
# sum = 0
# maxvalue = 255
# for i in xrange(255,0,-1):
# sum += hist[i]
# if sum > nHotPixels:
# maxvalue = i
# break
# if no override value given, scan down histogram from hot pixel value 255,
# set max level to be next lowest value
if maxvalue is None:
maxvalue = 254
for i in xrange(254,0,-1):
# if hist[i]>0:
# see config.py for more info
if hist[i] > config.adjustHistogramHotPixelCountCutoff:
maxvalue = i
break
# print maxvalue
maxvalue = maxvalue * 128
# set values > maxvalue to maxvalue
# see http://docs.scipy.org/doc/numpy/reference/generated/numpy.clip.html
np.clip(im, 0, maxvalue, im)
# convert 16-bit to 8-bit if needed (otherwise the histogram stretching gets posterized)
if type(im[0][0])==np.uint16:
# stretch image values to brightest amount
im = cv2.normalize(im, None, 0, 255, cv2.NORM_MINMAX)
# max level in the 16-bit image is 32767, and (/ 32767 128) = 255
# im = im / 128 # this can be dividing it by too much - using normalize is safer
im = np.array(im, np.uint8)
return im
# def adjustImageFile(infile, outfile, doStretchHistogram=True):
def adjustImageFile(infile, outfile, maxvalue=None):
"""
Adjust the given image file and save it to outfile - stretch histogram and rotate 180deg.
"""
# need ANYDEPTH flag as the pngs are 16-bit
im = cv2.imread(infile, cv2.IMREAD_GRAYSCALE | cv2.IMREAD_ANYDEPTH)
# stretch the histogram to bring up the brightness levels (the CALIB images are dark)
# if doStretchHistogram:
# im = stretchHistogram(im)
im = stretchHistogram16to8bit(im, maxvalue)
# rotate image by 180
im = np.rot90(im, 2)
retval = imwrite(outfile, im)
return retval
def show(im, title='cv2 image - press esc to continue'):
"Show a cv2 image and wait for a keypress"
if im.shape[1]>680:
im = resizeImage(im,int(im.shape[1]*0.75),int(im.shape[0]*0.75)) # might be nonsquare
cv2.imshow(title, im)
cv2.waitKey(0)
cv2.destroyAllWindows()
def shiftImage(im, dx, dy):
"""
Shift the image by dx, dy using an Affine matrix.
Note: image dimensions are kept the same - the image is just shifted out of frame.
"""
M = np.array([[1,0,dx],[0,1,dy]], np.float)
rows, cols = im.shape[:2]
# note order of cols, rows -
im = cv2.warpAffine(im, M, (cols, rows), flags = cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
return im
#. make this more generic - eg pass in set of images to align, return set of displacements
# could call it getChannelAlignments
def alignChannels(channels):
"attempt to align the images in the given channel arrays"
# print channels
# print [ch[2:-1] for ch in channels if ch]
im0 = channels[0][config.colChannelIm]
im1 = channels[1][config.colChannelIm]
assert not im0 is None
assert not im1 is None
dx,dy,alignmentOk = getImageAlignment(im0, im1)
if alignmentOk:
channels[1][config.colChannelX] = dx
channels[1][config.colChannelY] = dy
if channels[2]:
im2 = channels[2][config.colChannelIm]
assert not im2 is None
dx,dy,alignmentOk = getImageAlignment(im0, im2)
if alignmentOk:
channels[2][config.colChannelX] = dx
channels[2][config.colChannelY] = dy
# for channel in channels:
# if channel: print channel[2:-1]
return channels
#. refactor
def getCanvasSizeForChannels(channels):
"given an array of channels, return size of canvas that would contain them all"
xmin = 0; xmax = 799; ymin = 0; ymax = 799 #.params
for row in channels:
if row:
x = row[config.colChannelX] if len(row)>config.colChannelX else 0
y = row[config.colChannelY] if len(row)>config.colChannelY else 0
if x < xmin: xmin = x
if x+799 > xmax: xmax = x+799 #.param
if y < ymin: ymin = y
if y+799 > ymax: ymax = y+799 #.param
w = xmax-xmin+1; h = ymax-ymin+1
enlarged = (w!=800) or (h!=800) #.param
return w,h,xmin,ymin,enlarged
#. refactor
def combineChannels(channels, optionAlign=False):
"""
Combine the given channels and return a single cv2 image.
channels is an array of [fileId, filter, filename, weight, x, y]
eg channels = [
['c1234','Orange','composites/orange.png',1,0,0],
['c1235','Green','composites/green.png',0.8,30,40],
['c1236','Blue','composites/blue.png',0.9,50,66],
]
If only one channel included will return a b/w image.
If missing a channel will use a blank/black image for that channel.
If optionAlign is True will attempt to align channels - x,y values
are included in the return channels array.
Returns im, channels.
"""
# print channels
# if just one channel then return a bw image
if len(channels)==1:
filename = channels[0][config.colChannelFilename]
gray = cv2.imread(filename, cv2.IMREAD_GRAYSCALE)
if optionAlign:
channels[0][config.colChannelX] = 0
channels[0][config.colChannelY] = 0
return gray, channels
# # find size of canvas that will contain all images
# w,h,enlarged = getCanvasSizeForChannels(channels)
# # get images for each channel
# rowRed = None
# rowGreen = None
# rowBlue = None
# for row in channels:
# filename = row[colFilename]
# # note: this returns None if filename is invalid - doesn't throw an error
# #. this is wasteful - might not even use this file
# im = cv2.imread(filename, cv2.IMREAD_GRAYSCALE)
# # apply weight if necessary
# weight = row[colWeight] if len(row)>colWeight else 1.0
# if weight!=1.0: im = cv2.multiply(im,weight)
# # if canvas needs to be enlarged, do so
# if enlarged:
# canvas = np.zeros((h,w), np.uint8) # 0-255
# x = row[config.colChannelX] if len(row)>config.colChannelX else 0
# y = row[config.colChannelY] if len(row)>config.colChannelY else 0
# # print xmin,x,ymin,y
# # copy image into canvas at right point
# canvas[y-ymin:y-ymin+800, x-xmin:x-xmin+800] = im
# im = canvas
# # show(im)
# row.append(im)
# # now assign the row to one of the available channels
# # eventually would like something more accurate than just rgb.
# # and note: the last one in the set of channels wins.
# filter = row[config.colChannelFilter]
# if filter in ['Orange']:
# rowRed = row
# if filter in ['Green']:
# rowGreen = row
# if filter in ['Blue','Violet','Uv','Ch4_Js','Ch4_U']:
# rowBlue = row
# # assign a blank image if missing a channel
# blank = np.zeros((h,w), np.uint8)
# imRed = rowRed[colIm] if rowRed else blank
# imGreen = rowGreen[colIm] if rowGreen else blank
# imBlue = rowBlue[colIm] if rowBlue else blank
# # merge channels - BGR for cv2
# print imBlue.shape
# print imGreen.shape
# print imRed.shape
# # if imBlue.shape[0]!=800: imBlue = resizeImage(imBlue,800,800)
# # if imGreen.shape[0]!=800: imGreen = resizeImage(imGreen,800,800)
# # if imRed.shape[0]!=800: imRed = resizeImage(imRed,800,800)
# im = cv2.merge((imBlue, imGreen, imRed))
# # show(im)
# get dictionary of filters
d = {}
for row in channels:
filter = row[config.colChannelFilter]
d[filter] = row
# a little dictionary fn
def dget(d, skeys):
"pop a value from dictionary d, trying all keys in skeys"
if len(d)>0:
keys = skeys.split(',')
for key in keys:
value = d.pop(key, None)
if value:
return value
return None
# first pass - assign primary colors, if available
channelBlue = dget(d,'Blue')
channelRed = dget(d,'Orange')
channelGreen = dget(d,'Green')
# second pass - choose from some secondary options
# Ch4 are in infrared
if channelBlue is None: channelBlue = dget(d,'Violet,Uv,Ch4_Js,Ch4_U,Green,Orange')
if channelRed is None: channelRed = dget(d,'Ch4_Js,Ch4_U,Blue,Violet,Uv,Green')
if channelGreen is None: channelGreen = dget(d,'Ch4_Js,Ch4_U,Orange,Blue,Violet,Uv')
# third pass - anything can use the clear channel
blankrow = ['blank','Blank','blank.jpg',1,0,0]
if channelBlue is None: channelBlue = d.get('Clear') or blankrow
if channelRed is None: channelRed = d.get('Clear') or blankrow
if channelGreen is None: channelGreen = d.get('Clear') or blankrow
# get images
blank = np.zeros((800,800), np.uint8) #.params
for row in [channelBlue, channelRed, channelGreen]:
if row:
# print row
filename = row[config.colChannelFilename]
im = cv2.imread(filename, cv2.IMREAD_GRAYSCALE)
if im is None: im = blank
# apply weight if necessary
weight = row[config.colChannelWeight]
if weight!=1.0: im = cv2.multiply(im,weight)
#. handle this
# # if canvas needs to be enlarged, do so
# if enlarged:
# canvas = np.zeros((h,w), np.uint8) # 0-255
# x = row[config.colChannelX] if len(row)>config.colChannelX else 0
# y = row[config.colChannelY] if len(row)>config.colChannelY else 0
# # print xmin,x,ymin,y
# # copy image into canvas at right point
# canvas[y-ymin:y-ymin+800, x-xmin:x-xmin+800] = im
# im = canvas
# # show(im)
# stick the image on the end of the row (colIm)
row.append(im)
# # fourth pass - assume we have at least 2 channels at this point,
# # so try synthesizing a third.
# # . this doesn't work very well - better to have a dedicated colorize step
# imRed = channelRed[config.colChannelIm] if channelRed else None
# imGreen = channelGreen[config.colChannelIm] if channelGreen else None
# imBlue = channelBlue[config.colChannelIm] if channelBlue else None
# if imBlue is None: imBlue = (imRed + imGreen) / 2
# if imRed is None: imRed = (imBlue + imGreen) / 2
# if imGreen is None: imGreen = (imRed + imBlue) / 2
# attempt to align channels
if optionAlign:
channels = alignChannels([channelBlue, channelRed, channelGreen])
# find size of canvas that will contain all images
w,h,xmin,ymin,enlarged = getCanvasSizeForChannels(channels)
# print w,h,xmin,ymin,enlarged
# if canvas needs to be enlarged, do so, and position each channel correctly
if enlarged:
for row in channels:
if row: #.remove
im = row[config.colChannelIm]
x = row[config.colChannelX]
y = row[config.colChannelY]
im = shiftImage(im, x, y)
row[config.colChannelIm] = im
# assign a blank image if missing a channel
blank = np.zeros((h,w), np.uint8)
imRed = channelRed[config.colChannelIm] if channelRed else blank
imGreen = channelGreen[config.colChannelIm] if channelGreen else blank
imBlue = channelBlue[config.colChannelIm] if channelBlue else blank
# merge channels
# print imBlue.shape
# print imGreen.shape
# print imRed.shape
im = cv2.merge((imBlue, imGreen, imRed)) # BGR for cv2
# show(im)
# scale image to 800x800
if enlarged:
im = resizeImage(im, 800, 800) #.params
# show(im)
return im, channels
def drawCircle(im, circle, color = (0,255,0)):
"""
Draw a circle on the given cv2 image.
Note: circle is (x,y,radius), color is (b,g,r).
"""
(x,y,r) = circle
lineWidth = 1
cv2.circle(im, (x,y), r, color, lineWidth)
def gray2rgb(im):
"convert a gray cv2 image to rgb, return new image"
im = cv2.cvtColor(im, cv2.COLOR_GRAY2RGB)
return im
def rgb2gray(im):
"convert an rgb image to gray, return new image"
im = cv2.cvtColor(im, cv2.COLOR_RGB2GRAY)
return im
def drawBoundingBox(im, boundingBox):
"draw a box on image, return new image"
[x1,y1,x2,y2] = boundingBox
imbox = np.copy(im)
imbox = cv2.cvtColor(imbox, cv2.COLOR_GRAY2RGB)
cv2.rectangle(imbox, (x1,y1),(x2,y2), (255,0,0), 2)
return imbox
def findCircle(im, expectedRadius=None):
"""
Find best circle in given image, with optional expectedRadius of target.
Returns circle as (x,y,r)
"""
# set Hough circle detection parameters
# Note: internally the HoughCircles function calls the Canny edge detector
# only available method now
# method = cv2.cv.CV_HOUGH_GRADIENT # for OpenCV v2
method = cv2.HOUGH_GRADIENT # if get error here, upgrade to OpenCV v3
# size of accumulator space relative to input image
dp = config.houghAccumulatorSize # eg 1.0
# distance between circles
minDist = config.houghMinDistanceBetweenCircles # eg 200px
# First method-specific parameter. In case of CV_HOUGH_GRADIENT,
# it is the higher threshold of the two passed to the Canny() edge
# detector (the lower one is twice smaller).
# higher value means edges need to be sharper
# this value will be lowered if no circles found
canny_threshold = config.houghCannyUpperThreshold # eg 200
# the accumulator threshold for the circle centers at the detection
# stage. The smaller it is, the more false circles may be detected. Circles
# corresponding to the larger accumulator values, will be returned first.
# This will set how many edge points it needs to find to
# declare that it's found a circle. Again, too high will detect nothing, too
# low will declare anything to be a circle. The ideal value of param 2 will
# be related to the circumference of the circles.
#. so should be proportional to the expectedRadius?
acc_threshold = config.houghAccumulatorThreshold # eg 10
# get search radii
if expectedRadius:
pct = config.houghRadiusSearchPercent # eg 10
minRadius = int((1-float(pct)/100) * expectedRadius)
maxRadius = int((1+float(pct)/100) * expectedRadius)
else:
minRadius = 0
maxRadius = 0
# look for circles, lowering canny threshold if can't find any (ie assume target is dim)
circles = None
while circles is None:
circles = cv2.HoughCircles(im, method, dp, minDist,
param1 = canny_threshold,
param2 = acc_threshold,
minRadius = minRadius,
maxRadius = maxRadius)
if circles is None:
canny_threshold = int(canny_threshold / 2)
# log.log('reducing canny threshold to',canny_threshold)
if canny_threshold < 20: #. param
break
# draw canny edges
if config.debugImageTitle:
upper = canny_threshold
lower = upper / 2 # this is what HoughCircles uses
imedges = cv2.Canny(im, lower, upper)
cv2.imwrite(config.debugImageTitle + '_cannyedges.jpg', imedges)
if circles is None:
# log.log('no circles found')
circle = None
else:
circles = circles[0,:] # extract array
circle = circles[0]
circle = np.round(circle).astype('int') # round all values to ints
# draw circles
if config.debugImageTitle:
im = gray2rgb(im)
for circ in circles:
circ = np.round(circ).astype('int')
drawCircle(im, circ, (0,0,255)) # red
drawCircle(im, circle) # green
cv2.imwrite(config.debugImageTitle + '_circles.jpg', im)
return circle # (x,y,r)
def centerImage(im, boundingBox):
"center image on bounding box, crop to it, return new image"
[x1,y1,x2,y2] = boundingBox
cx = int((x1+x2)/2.0)
cy = int((y1+y2)/2.0)
# reverse these
imwidth = im.shape[1]
imheight = im.shape[0]
# make a bigger canvas to place image im on
newsize = (imheight * 2, imwidth * 2)
canvas = np.zeros(newsize, np.uint8) # defaults to float
# put image on canvas centered on bounding box
# eg canvas[800-cx:1600-cx, 800-cy:1600-cy] = np.array(im)
canvas[imheight-cy : imheight-cy+imheight, imwidth-cx : imwidth-cx+imwidth] = im
# crop canvas to original image size
# eg imcrop = canvas[400:1200, 400:1200]
x1 = int(imwidth/2)
y1 = int(imheight/2)
# imcrop = canvas[x1:x1+imwidth, y1:y1+imheight]
imcrop = canvas[y1:y1+imheight, x1:x1+imwidth]
return imcrop
def findBoundingBoxByCircle(im, radius):
"Find the bounding box enclosing the best circle in image and return it, or None."
circle = findCircle(im, radius)
if not circle is None:
(x,y,r) = circle
x1 = x-r
x2 = x+r
y1 = y-r
y2 = y+r
boundingBox = [x1,y1,x2,y2]
else:
# if no circles just return the whole image
# x1 = 0
# x2 = im.shape[1] - 1
# y1 = 0
# y2 = im.shape[0] - 1
boundingBox = None
return boundingBox
def findBoundingBoxByBlob(im):
"Find the largest blob in the given image and return the bounding box [x1,y1,x2,y2]"
# threshold to binary image
# b = 1*(im>blobThreshold)
# adaptive thresholding -
b = cv2.adaptiveThreshold(im, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY_INV,
config.blobAdaptiveThresholdSize, # eg 9
config.blobAdaptiveThresholdConstant) # eg 6
# find and label blob objects
labels, nobjs = ndimage.measurements.label(b)
# if config.drawBinaryImage:
if config.debugImageTitle:
cv2.imwrite(config.debugImageTitle + '_binaryimage.jpg', b)
# find position of objects
# http://docs.scipy.org/doc/scipy-0.16.1/reference/generated/
# scipy.ndimage.measurements.find_objects.html
# http://stackoverflow.com/questions/22103572/how-to-find-the-rectangles-in-an-image
blobs = ndimage.find_objects(labels)
# by default, if no blobs just return the whole image
x1 = 0
x2 = im.shape[1] - 1
y1 = 0
y2 = im.shape[0] - 1
# find largest object, if any
if len(blobs)>0:
areamax = 0
largestblob = None
for blob in blobs:
width = blob[1].stop - blob[1].start
height = blob[0].stop - blob[0].start
area = width * height
if area>areamax:
# check for min width and height so don't pick up edge artifacts
if width>1 and height>1:
#. try larger and check if actually on edge
# if width>2 and height>2:
# if width>3 and height>3:
areamax = area
largestblob = blob
# get bounding box
if largestblob:
x1 = largestblob[1].start
x2 = largestblob[1].stop
y1 = largestblob[0].start
y2 = largestblob[0].stop
boundingBox = [x1,y1,x2,y2]
# draw bounding box
if config.debugImageTitle:
imbox = drawBoundingBox(im, boundingBox)
cv2.imwrite(config.debugImageTitle + '_blobboundingbox.jpg', imbox)
return boundingBox
def findBoundingBox(im, radius):
"Find bounding box with expected target radius. Returns [x1,y1,x2,y2]"
# use blob detector if radius<threshold
if radius < config.blobRadiusMax: # eg 10 pixels
boundingBox = findBoundingBoxByBlob(im)
else: # use hough to find circle
boundingBox = findBoundingBoxByCircle(im, radius)
# if couldn't find a circle, just use the blob bounding box for approximate answer
if boundingBox is None:
boundingBox = findBoundingBoxByBlob(im)
return boundingBox
if __name__ == "__main__":
import lib
orange = '../'+lib.getFilepath('adjust','7206','C2684338','Clear')
green = '../'+lib.getFilepath('adjust','7206','C2684342','Green')
blue = '../'+lib.getFilepath('adjust','7206','C2684340','Violet')
print orange
channels = [
['Orange',orange,0.7,120,-65],
['Green',green,1,150,20],
['Blue',blue,1,0,0],
]
im = combineChannels(channels)
show(im)
cv2.imwrite('foo.jpg',im)
|
bburns/PyVoyager
|
src/libimg.py
|
Python
|
mit
| 52,860
|
[
"Gaussian"
] |
dba47f7f7a796f9b6d5493e4abd271b31de5d8f071f16203a75946fc761d7cd4
|
"""
The Job Sanity Agent accepts all jobs from the Job
receiver and screens them for the following problems:
- Output data already exists
- Problematic JDL
- Jobs with too much input data e.g. > 100 files
- Jobs with input data incorrectly specified e.g. castor:/
- Input sandbox not correctly uploaded.
"""
__RCSID__ = "$Id$"
import re
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.WorkloadManagementSystem.Client.SandboxStoreClient import SandboxStoreClient
from DIRAC.WorkloadManagementSystem.Executor.Base.OptimizerExecutor import OptimizerExecutor
class JobSanity(OptimizerExecutor):
"""
The specific Optimizer must provide the following methods:
- optimizeJob() - the main method called for each job
and it can provide:
- initializeOptimizer() before each execution cycle
"""
@classmethod
def initializeOptimizer(cls):
"""Initialize specific parameters for JobSanityAgent.
"""
cls.sandboxClient = SandboxStoreClient(useCertificates=True)
return S_OK()
def optimizeJob(self, jid, jobState):
""" This method controls the order and presence of
each sanity check for submitted jobs. This should
be easily extended in the future to accommodate
any other potential checks.
"""
# Job JDL check
result = jobState.getAttribute('JobType')
if not result['OK']:
return result
jobType = result['Value'].lower()
result = jobState.getManifest()
if not result['OK']:
return result
manifest = result['Value']
# Input data check
if self.ex_getOption('InputDataCheck', True):
voName = manifest.getOption("VirtualOrganization", "")
if not voName:
return S_ERROR("No VirtualOrganization defined in manifest")
result = self.checkInputData(jobState, jobType, voName)
if not result['OK']:
return result
self.jobLog.info("%s LFNs" % result['Value'])
# Input Sandbox uploaded check
if self.ex_getOption('InputSandboxCheck', True):
result = self.checkInputSandbox(jobState, manifest)
if not result['OK']:
return result
self.jobLog.info("Assigned %s ISBs" % result['Value'])
return self.setNextOptimizer(jobState)
def checkInputData(self, jobState, jobType, voName):
"""This method checks both the amount of input
datasets for the job and whether the LFN conventions
are correct.
"""
result = jobState.getInputData()
if not result['OK']:
self.jobLog.warn('Failed to get input data from JobDB')
self.jobLog.warn(result['Message'])
return S_ERROR("Input Data Specification")
data = result['Value'] # seems to be [''] when null, which isn't an empty list ;)
data = [lfn.strip() for lfn in data if lfn.strip()]
if not data:
return S_OK(0)
self.jobLog.debug('Input data requirement will be checked')
self.jobLog.debug('Data is:\n\t%s' % "\n\t".join(data))
voRE = re.compile("^(LFN:)?/%s/" % voName)
for lfn in data:
if not voRE.match(lfn):
return S_ERROR("Input data not correctly specified")
if lfn.find("//") > -1:
return S_ERROR("Input data contains //")
# only check limit for user jobs
if jobType == 'user':
maxLFNs = self.ex_getOption('MaxInputDataPerJob', 100)
if len(data) > maxLFNs:
return S_ERROR("Exceeded Maximum Dataset Limit (%s)" % maxLFNs)
return S_OK(len(data))
def checkInputSandbox(self, jobState, manifest):
"""The number of input sandbox files, as specified in the job
JDL are checked in the JobDB.
"""
result = jobState.getAttributes(['Owner', 'OwnerDN', 'OwnerGroup', 'DIRACSetup'])
if not result['OK']:
return result
attDict = result['Value']
ownerName = attDict['Owner']
if not ownerName:
ownerDN = attDict['OwnerDN']
if not ownerDN:
return S_ERROR("Missing OwnerDN")
result = Registry.getUsernameForDN(ownerDN)
if not result['OK']:
return result
ownerName = result['Value']
ownerGroup = attDict['OwnerGroup']
if not ownerGroup:
return S_ERROR("Missing OwnerGroup")
jobSetup = attDict['DIRACSetup']
if not jobSetup:
return S_ERROR("Missing DIRACSetup")
isbList = manifest.getOption('InputSandbox', [])
sbsToAssign = []
for isb in isbList:
if isb.find("SB:") == 0:
self.jobLog.info("Found a sandbox", isb)
sbsToAssign.append((isb, "Input"))
numSBsToAssign = len(sbsToAssign)
if not numSBsToAssign:
return S_OK(0)
self.jobLog.info("Assigning %s sandboxes on behalf of %s@%s" % (numSBsToAssign, ownerName, ownerGroup))
result = self.sandboxClient.assignSandboxesToJob(jobState.jid, sbsToAssign, ownerName, ownerGroup, jobSetup)
if not result['OK']:
self.jobLog.error("Could not assign sandboxes in the SandboxStore")
return S_ERROR("Cannot assign sandbox to job")
assigned = result['Value']
if assigned != numSBsToAssign:
self.jobLog.error("Could not assign all sandboxes (%s). Only assigned %s" % (numSBsToAssign, assigned))
return S_OK(numSBsToAssign)
|
petricm/DIRAC
|
WorkloadManagementSystem/Executor/JobSanity.py
|
Python
|
gpl-3.0
| 5,229
|
[
"DIRAC"
] |
b39d2512f4e2efd4aa020f45897e04af54db72f1811f76dff160d0de4d1e28aa
|
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
#
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# @END LICENSE
#
import datetime
import os
import socket
from . import core
from .metadata import __version__, version_formatter
time_string = datetime.datetime.now().strftime('%A, %d %B %Y %I:%M%p')
pid = os.getpid()
def sizeof_fmt(num, suffix='B'):
for unit in ['','Ki','Mi','Gi','Ti','Pi','Ei','Zi']:
if abs(num) < 1024.0:
return "%3.1f %s%s" % (num, unit, suffix)
num /= 1024.0
return "%.1f %s%s" % (num, 'Yi', suffix)
def print_header():
driver_info = version_formatter("""{version} {release}""")
git_info = version_formatter("""{{{branch}}} {githash} {clean}""")
datadir = core.get_datadir()
memory = sizeof_fmt(core.get_memory())
hostname = socket.gethostname()
threads = str(core.get_num_threads())
header = """
-----------------------------------------------------------------------
Psi4: An Open-Source Ab Initio Electronic Structure Package
Psi4 {}
Git: Rev {}
D. G. A. Smith, L. A. Burns, A. C. Simmonett, R. M. Parrish,
M. C. Schieber, R. Galvelis, P. Kraus, H. Kruse, R. Di Remigio,
A. Alenaizan, A. M. James, S. Lehtola, J. P. Misiewicz, M. Scheurer,
R. A. Shaw, J. B. Schriber, Y. Xie, Z. L. Glick, D. A. Sirianni,
J. S. O'Brien, J. M. Waldrop, A. Kumar, E. G. Hohenstein,
B. P. Pritchard, B. R. Brooks, H. F. Schaefer III, A. Yu. Sokolov,
K. Patkowski, A. E. DePrince III, U. Bozkaya, R. A. King,
F. A. Evangelista, J. M. Turney, T. D. Crawford, C. D. Sherrill,
J. Chem. Phys. 152(18) 184108 (2020). https://doi.org/10.1063/5.0006002
Additional Code Authors
E. T. Seidl, C. L. Janssen, E. F. Valeev, M. L. Leininger,
J. F. Gonthier, R. M. Richard, H. R. McAlexander, M. Saitow, X. Wang,
P. Verma, M. H. Lechner, and A. Jiang
Previous Authors, Complete List of Code Contributors,
and Citations for Specific Modules
https://github.com/psi4/psi4/blob/master/codemeta.json
https://github.com/psi4/psi4/graphs/contributors
http://psicode.org/psi4manual/master/introduction.html#citing-psifour
-----------------------------------------------------------------------
Psi4 started on: {}
Process ID: {}
Host: {}
PSIDATADIR: {}
Memory: {}
Threads: {}
""".format(driver_info, git_info, time_string, pid, hostname, datadir, memory, threads)
core.print_out(header)
|
psi4/psi4
|
psi4/header.py
|
Python
|
lgpl-3.0
| 3,388
|
[
"Psi4"
] |
5fe033778a11b0803a814a3b4e906732bb0de2943d87c920476dcbdb02b8b121
|
# Copyright 2019 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ==============================================================================
"""Keras layers that implement explicit (approximate) kernel feature maps."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import six
from tensorflow.python.framework import dtypes
from tensorflow.python.framework import ops
from tensorflow.python.framework import tensor_shape
from tensorflow.python.keras import initializers
from tensorflow.python.keras.engine import base_layer
from tensorflow.python.keras.engine import input_spec
from tensorflow.python.ops import gen_math_ops
from tensorflow.python.ops import init_ops
from tensorflow.python.ops import nn
_SUPPORTED_RBF_KERNEL_TYPES = ['gaussian', 'laplacian']
class RandomFourierFeatures(base_layer.Layer):
r"""Layer that maps its inputs using random Fourier features.
This layer implements a feature map \\(\phi: \mathbb{R}^d \rightarrow
\mathbb{R}^D\\) which approximates shift-invariant kernels. A kernel function
K(x, y) defined over \\(\mathbb{R}^d x \mathbb{R}^d\\) is shift-invariant if
K(x, y) = k(x-y) for some function defined over \\(\mathbb{R}^d\\). Many
popular Radial Basis Functions (in short RBF), including gaussian and
laplacian kernels are shift-invariant.
The layer approximates a (shift invariant) kernel K in the following sense:
up to a scaling factor, for all inputs \\(x, y \in \mathbb{R}^d\\)
\\(\phi(x)^T \cdot \phi(y) \approx K(x, y)\\)
The implementation of this layer is based on the following paper:
"Random Features for Large-Scale Kernel Machines" by Ali Rahimi and Ben Recht.
(link: https://people.eecs.berkeley.edu/~brecht/papers/07.rah.rec.nips.pdf)
The distribution from which the parameters of the random features map (layer)
are sampled, determines which shift-invariant kernel the layer approximates
(see paper for more details). The users can use the distribution of their
choice. Due to their popularity, the layer supports the out-of-the-box
approximation of the following RBF kernels:
- Gaussian: \\(K(x, y) = e^{-\frac{\|x-y\|_2^2}{2 \cdot scale^2}}\\)
- Laplacian: \\(K(x, y) = e^{-\frac{\|x-y\|_1}{scale}}\\)
NOTE: Unlike the map described in the paper and the scikit-learn
implementation, the output of this layer does not apply the sqrt(2/D)
normalization factor.
Usage for ML: Typically, this layer is used to "kernelize" linear models by
applying a non-linear transformation (this layer) to the input features and
then training a linear model on top of the transformed features. Depending on
the loss function of the linear model, the composition of this layer and the
linear model results to models that are equivalent (up to approximation) to
kernel SVMs (for hinge loss), kernel logistic regression (for logistic loss),
kernel linear regression (for squared loss) etc.
Example of building a kernel multinomial logistic regression model with
Gaussian kernel in keras:
```python
random_features_layer = RandomFourierFeatures(
output_dim=500,
kernel_initializer='gaussian',
scale=5.0,
...)
model = tf.keras.models.Sequential()
model.add(random_features_layer)
model.add(tf.keras.layers.Dense(units=num_classes, activation='softmax')
model.compile(
loss=tf.keras.losses.categorical_crossentropy, optimizer=..., metrics=...)
```
To use another kernel, replace the layer creation command with:
```python
random_features_layer = RandomFourierFeatures(
output_dim=500,
kernel_initializer=<my_initializer>,
scale=...,
...)
```
Arguments:
output_dim: Positive integer, the dimension of the layer's output, i.e., the
number of random features used to approximate the kernel.
kernel_initializer: Determines the distribution of the parameters of the
random features map (and therefore the kernel approximated by the layer).
It can be either a string or an instance of TensorFlow's Initializer
class. Currently only 'gaussian' and 'laplacian' are supported as string
initializers (case insensitive). Note that these parameters are not
trainable.
scale: For gaussian and laplacian kernels, this corresponds to a scaling
factor of the corresponding kernel approximated by the layer (see concrete
definitions above). When provided, it should be a positive float. If None,
the implementation chooses a default value (1.0 typically). Both the
approximation error of the kernel and the classification quality are
sensitive to this parameter. If trainable is set to True, this parameter
is learned end-to-end during training and the provided value serves as an
initialization value.
NOTE: When this layer is used to map the initial features and then the
transformed features are fed to a linear model, by making `scale`
trainable, the resulting optimization problem is no longer convex (even
if the loss function used by the linear model is convex).
trainable: Whether the scaling parameter of th layer is trainable. Defaults
to False.
name: name for the RandomFourierFeatures layer.
Raises:
ValueError: if output_dim or stddev are not positive or if the provided
kernel_initializer is not supported.
"""
def __init__(self,
output_dim,
kernel_initializer='gaussian',
scale=None,
trainable=False,
name=None,
**kwargs):
if output_dim <= 0:
raise ValueError(
'`output_dim` should be a positive integer. Given: {}.'.format(
output_dim))
if isinstance(kernel_initializer, six.string_types):
if kernel_initializer.lower() not in _SUPPORTED_RBF_KERNEL_TYPES:
raise ValueError(
'Unsupported kernel type: \'{}\'. Supported kernel types: {}.'
.format(kernel_initializer, _SUPPORTED_RBF_KERNEL_TYPES))
if scale is not None and scale <= 0.0:
raise ValueError('When provided, `scale` should be a positive float. '
'Given: {}.'.format(scale))
super(RandomFourierFeatures, self).__init__(
trainable=trainable, name=name, **kwargs)
self.output_dim = output_dim
self.kernel_initializer = kernel_initializer
self.scale = scale
def build(self, input_shape):
input_shape = tensor_shape.TensorShape(input_shape)
# TODO(sibyl-vie3Poto): Allow higher dimension inputs. Currently the input is expected
# to have shape [batch_size, dimension].
if input_shape.rank != 2:
raise ValueError(
'The rank of the input tensor should be 2. Got {} instead.'.format(
input_shape.ndims))
if input_shape.dims[1].value is None:
raise ValueError(
'The last dimension of the inputs to `RandomFourierFeatures` '
'should be defined. Found `None`.')
self.input_spec = input_spec.InputSpec(
ndim=2, axes={1: input_shape.dims[1].value})
input_dim = input_shape.dims[1].value
kernel_initializer = _get_random_features_initializer(
self.kernel_initializer, shape=(input_dim, self.output_dim))
unscaled_kernel = self.add_weight(
name='unscaled_random_features',
shape=(input_dim, self.output_dim),
dtype=dtypes.float32,
initializer=kernel_initializer,
trainable=False)
self.bias = self.add_weight(
name='random_features_bias',
shape=(self.output_dim,),
dtype=dtypes.float32,
initializer=init_ops.random_uniform_initializer(
minval=0.0, maxval=2 * np.pi, dtype=dtypes.float32),
trainable=False)
if self.scale is None:
self.scale = _get_default_scale(self.kernel_initializer, input_dim)
scale = self.add_weight(
name='random_features_scale',
shape=(1,),
dtype=dtypes.float32,
initializer=init_ops.constant_initializer(self.scale),
trainable=True,
constraint='NonNeg')
self.kernel = (1.0 / scale) * unscaled_kernel
super(RandomFourierFeatures, self).build(input_shape)
def call(self, inputs):
inputs = ops.convert_to_tensor(inputs, dtype=self.dtype)
inputs = gen_math_ops.cast(inputs, dtypes.float32)
outputs = gen_math_ops.mat_mul(inputs, self.kernel)
outputs = nn.bias_add(outputs, self.bias)
return gen_math_ops.cos(outputs)
def compute_output_shape(self, input_shape):
input_shape = tensor_shape.TensorShape(input_shape)
input_shape = input_shape.with_rank(2)
if input_shape.dims[-1].value is None:
raise ValueError(
'The innermost dimension of input shape must be defined. Given: %s' %
input_shape)
return input_shape[:-1].concatenate(self.output_dim)
def get_config(self):
kernel_initializer = self.kernel_initializer
if isinstance(self.kernel_initializer, init_ops.Initializer):
kernel_initializer = initializers.serialize(self.kernel_initializer)
config = {
'output_dim': self.output_dim,
'kernel_initializer': kernel_initializer,
'scale': self.scale,
}
base_config = super(RandomFourierFeatures, self).get_config()
return dict(list(base_config.items()) + list(config.items()))
def _get_random_features_initializer(initializer, shape):
"""Returns Initializer object for random features."""
def _get_cauchy_samples(loc, scale, shape):
probs = np.random.uniform(low=0., high=1., size=shape)
return loc + scale * np.tan(np.pi * (probs - 0.5))
random_features_initializer = initializer
if isinstance(initializer, six.string_types):
if initializer.lower() == 'gaussian':
random_features_initializer = init_ops.random_normal_initializer(
stddev=1.0)
elif initializer.lower() == 'laplacian':
random_features_initializer = init_ops.constant_initializer(
_get_cauchy_samples(loc=0.0, scale=1.0, shape=shape))
else:
raise ValueError(
'Unsupported kernel type: \'{}\'. Supported kernel types: {}.'.format(
random_features_initializer, _SUPPORTED_RBF_KERNEL_TYPES))
return random_features_initializer
def _get_default_scale(initializer, input_dim):
if (isinstance(initializer, six.string_types) and
initializer.lower() == 'gaussian'):
return np.sqrt(input_dim / 2.0)
return 1.0
|
ghchinoy/tensorflow
|
tensorflow/python/keras/layers/kernelized.py
|
Python
|
apache-2.0
| 11,044
|
[
"Gaussian"
] |
fc1c5b0e97069ab4217652c1258d692955564ae82a1ae4a3087342d18604f5b7
|
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergovernmental Organization or
# submit itself to any jurisdiction.
# Project website: http://blond.web.cern.ch/
'''
Test case for the synchrotron radiation routine.
Example for the FCC-ee at 175 GeV.
:Authors: **Juan F. Esteban Mueller**
'''
from __future__ import division
import matplotlib.pyplot as plt
import os
import numpy as np
from blond.input_parameters.ring import Ring
from blond.beam.beam import Beam, Electron
from blond.beam.distributions import matched_from_distribution_function
from blond.input_parameters.rf_parameters import RFStation
from blond.beam.profile import Profile
from blond.trackers.tracker import RingAndRFTracker, FullRingAndRF
from blond.synchrotron_radiation.synchrotron_radiation import SynchrotronRadiation
from scipy.constants import c, e, m_e
from blond.beam.profile import CutOptions
this_directory = os.path.dirname(os.path.realpath(__file__)) + '/'
try:
os.mkdir(this_directory + '../output_files')
except:
pass
try:
os.mkdir(this_directory + '../output_files/EX_13_fig')
except:
pass
# SIMULATION PARAMETERS -------------------------------------------------------
# Beam parameters
particle_type = Electron()
n_particles = int(1.7e11)
n_macroparticles = int(1e5)
sync_momentum = 175e9 # [eV]
distribution_type = 'gaussian'
emittance = 1.0
distribution_variable = 'Action'
# Machine and RF parameters
radius = 15915.49
gamma_transition = 377.96447
C = 2 * np.pi * radius # [m]
# Tracking details
n_turns = int(200)
n_turns_between_two_plots = 100
# Derived parameters
E_0 = m_e * c**2 / e # [eV]
tot_beam_energy = np.sqrt(sync_momentum**2 + E_0**2) # [eV]
momentum_compaction = 1 / gamma_transition**2 # [1]
# Cavities parameters
n_rf_systems = 1
harmonic_numbers = 133650
voltage_program = 10e9
phi_offset = np.pi
bucket_length = C / c / harmonic_numbers
# DEFINE RING------------------------------------------------------------------
n_sections = 2
general_params = Ring(np.ones(n_sections) * C/n_sections,
np.tile(momentum_compaction,(1,n_sections)).T,
np.tile(sync_momentum,(n_sections, n_turns+1)),
particle_type, n_turns, n_sections = n_sections)
RF_sct_par = []
for i in np.arange(n_sections)+1:
RF_sct_par.append(RFStation(general_params,
[harmonic_numbers], [voltage_program/n_sections],
[phi_offset], n_rf_systems, section_index=i) )
# DEFINE BEAM------------------------------------------------------------------
beam = Beam(general_params, n_macroparticles, n_particles)
# DEFINE SLICES----------------------------------------------------------------
number_slices = 500
cut_options = CutOptions(cut_left=0., cut_right=bucket_length, n_slices=number_slices)
slice_beam = Profile(beam, CutOptions = cut_options)
# DEFINE TRACKER---------------------------------------------------------------
longitudinal_tracker = []
for i in range(n_sections):
longitudinal_tracker.append(RingAndRFTracker(RF_sct_par[i],beam,Profile = slice_beam))
full_tracker = FullRingAndRF(longitudinal_tracker)
# BEAM GENERATION--------------------------------------------------------------
matched_from_distribution_function(beam, full_tracker, emittance=emittance,
distribution_type=distribution_type,
distribution_variable=distribution_variable
, seed=1000)
slice_beam.track()
# Synchrotron radiation objects without quantum excitation
rho = 11e3
SR = []
for i in range(n_sections):
SR.append(SynchrotronRadiation(general_params, RF_sct_par[i], beam, rho,
quantum_excitation=False, python=True))
SR[0].print_SR_params()
# ACCELERATION MAP-------------------------------------------------------------
map_ = []
for i in range(n_sections):
map_ += [longitudinal_tracker[i]] + [SR[i]]
map_ += [slice_beam]
# TRACKING + PLOTS-------------------------------------------------------------
avg_dt = np.zeros(n_turns)
std_dt = np.zeros(n_turns)
for i in range(n_turns):
for m in map_:
m.track()
avg_dt[i] = np.mean(beam.dt)
std_dt[i] = np.std(beam.dt)
## Fitting routines for synchrotron radiation damping
from scipy.optimize import curve_fit
def sine_exp_fit(x,y, **keywords):
try:
init_values = keywords['init_values']
offset = init_values[-1]
init_values[-1] = 0
except:
offset = np.mean(y)
# omega estimation using FFT
npoints = 12
y_fft = np.fft.fft(y-offset, 2**npoints)
omega_osc = (2.0 * np.pi * np.abs(y_fft[:2**(npoints-1)]).argmax() /
len(y_fft) / (x[1]-x[0]))
init_amp = (y.max()-y.min())/2.0
init_omega = omega_osc
init_values = [init_omega,0,init_amp,0,0]
popt, pcov = curve_fit(sine_exp_f, x, y-offset,p0=init_values)
popt[0] = np.abs(popt[0])
popt[2] = np.abs(popt[2])
popt[3] += offset
if np.isinf(pcov).any():
pcov = np.zeros([5,5])
return popt, pcov
def sine_exp_f(x, omega, phi, amp, offset, tau):
return offset + np.abs(amp)*np.sin(omega*x+phi)*np.exp(tau*x)
def exp_f(x, amp, offset, tau):
return offset + np.abs(amp)*np.exp(-np.abs(tau)*x)
# Fit of the bunch length
plt.figure(figsize=[6,4.5])
plt.plot( 1e12*4.0*std_dt,lw=2)
a,b = popt, pcov = curve_fit(exp_f, np.arange(len(std_dt)), 4.0*std_dt)
amp, offset, tau = a[0],a[1],a[2]
plt.plot(np.arange(len(std_dt)), 1e12*exp_f(np.arange(len(std_dt)), amp,
offset, np.abs(tau)), 'r--', lw=2, alpha=0.75)
plt.ylim(0,plt.ylim()[1])
plt.xlabel('Turns')
plt.ylabel('Bunch length [ps]')
plt.legend(('Simulation','Damping time: {0:1.1f} turns (fit)'.format(1 /
np.abs(tau))), loc=0, fontsize='medium')
plt.savefig(this_directory + '../output_files/EX_13_fig/bl_fit.png')
plt.close()
# Fit of the bunch position
a,b = sine_exp_fit(np.arange(len(avg_dt)),avg_dt)
omega, phi, amp, offset, tau = a[0],a[1],a[2],a[3],a[4]
plt.figure(figsize=[6,4.5])
plt.plot(avg_dt*1e9,lw=2)
plt.plot(np.arange(len(avg_dt)), sine_exp_f(np.arange(len(avg_dt)), omega, phi,
amp, offset, tau)*1e9, 'r--', lw=2, alpha=0.75)
plt.xlabel('Turns')
plt.ylabel('Bunch position [ns]')
plt.legend(('Simulation','Damping time: {0:1.1f} turns (fit)'.format(1 /
np.abs(tau))),loc=0,fontsize='medium')
plt.savefig(this_directory + '../output_files/EX_13_fig/pos_fit')
plt.close()
## WITH QUANTUM EXCITATION
n_turns = 200
# DEFINE RING------------------------------------------------------------------
n_sections = 10
general_params = Ring(np.ones(n_sections) * C/n_sections,
np.tile(momentum_compaction,(1,n_sections)).T,
np.tile(sync_momentum,(n_sections, n_turns+1)),
particle_type, n_turns, n_sections=n_sections)
RF_sct_par = []
for i in np.arange(n_sections)+1:
RF_sct_par.append(RFStation(general_params,
[harmonic_numbers], [voltage_program/n_sections],
[phi_offset], n_rf_systems, section_index=i) )
# DEFINE BEAM------------------------------------------------------------------
beam = Beam(general_params, n_macroparticles, n_particles)
# DEFINE SLICES----------------------------------------------------------------
cut_options = CutOptions(cut_left=0., cut_right=bucket_length, n_slices=number_slices)
slice_beam = Profile(beam, CutOptions = cut_options)
# DEFINE TRACKER---------------------------------------------------------------
longitudinal_tracker = []
for i in range(n_sections):
longitudinal_tracker.append(RingAndRFTracker(RF_sct_par[i],beam,Profile = slice_beam))
full_tracker = FullRingAndRF(longitudinal_tracker)
# BEAM GENERATION--------------------------------------------------------------
matched_from_distribution_function(beam, full_tracker, emittance=emittance,
distribution_type=distribution_type,
distribution_variable=distribution_variable
, seed=1000)
slice_beam.track()
# Redefine Synchrotron radiation objects with quantum excitation
SR = []
for i in range(n_sections):
SR.append(SynchrotronRadiation(general_params, RF_sct_par[i], beam, rho, python=False, seed=7))
# ACCELERATION MAP-------------------------------------------------------------
map_ = []
for i in range(n_sections):
map_ += [longitudinal_tracker[i]] + [SR[i]]
map_ += [slice_beam]
# TRACKING + PLOTS-------------------------------------------------------------
std_dt = np.zeros(n_turns)
std_dE = np.zeros(n_turns)
for i in range(n_turns):
for m in map_:
m.track()
std_dt[i] = np.std(beam.dt)
std_dE[i] = np.std(beam.dE)
plt.figure(figsize=[6,4.5])
plt.plot(1e-6*std_dE, lw=2)
plt.plot(np.arange(len(std_dE)), [1e-6*SR[0].sigma_dE*sync_momentum] *
len(std_dE), 'r--', lw=2)
print('Equilibrium energy spread = {0:1.3f} [MeV]'.format(1e-6 *
std_dE[-10:].mean()))
plt.xlabel('Turns')
plt.ylabel('Energy spread [MeV]')
plt.savefig(this_directory + '../output_files/EX_13_fig/std_dE_QE.png')
plt.close()
plt.figure(figsize=[6,4.5])
plt.plot(1e12*4.0*std_dt, lw=2)
print('Equilibrium bunch length = {0:1.3f} [ps]'.format(4e12 *
std_dt[-10:].mean()))
plt.xlabel('Turns')
plt.ylabel('Bunch length [ps]')
plt.savefig(this_directory + '../output_files/EX_13_fig/bl_QE.png')
plt.close()
print("Done!")
|
blond-admin/BLonD
|
__EXAMPLES/main_files/EX_13_synchrotron_radiation.py
|
Python
|
gpl-3.0
| 10,317
|
[
"Gaussian"
] |
18f5a64b714aa171108789bf8633e6f8fe756ecde9085e9168b45469251a2dc6
|
# will ``sample_submission`` to your submission filename.
from sample_submission import regressor
import numpy as np
def rmse(a, b):
"""
This function produces a point-wise root mean squared error error between ``a`` and ``b``
Args:
a: first input ndarray
b: second input ndarray
Returns:
numpy float: rmse error
Notes:
The grade that you will get will depend on this output. The lower this value, the higher
your grade.
"""
return np.sqrt(np.mean((a - b) ** 2))
class dataset_generator(object):
"""
Class that creates a random dataset. Note that for the grading of the project, this method
might be changed, although it's output format will not be. This implies we might use other
methods to create data. You must assume that the dataset will be blind and your machine is
capable of running any dataset.
Args:
dimensions: number of dimensions of dataset (optional, default randomly 15-30)
mu: mean of the gaussian with which we add noise (optional, default 0)
sigma: variance of the gaussian with which we add noise (optional, default 0.1)
"""
def __init__(self, **kwargs):
low = 15
high = 30
if 'dimensions' in kwargs.keys():
self.dimensions = kwargs['dimensions']
else:
self.dimensions = np.random.randint(low=low, high=high)
if 'mu' in kwargs.keys():
self.mu = kwargs['mu']
else:
self.mu = 0
if 'sigma' in kwargs.keys():
self.sigma = kwargs['sigma']
else:
self.sigma = 0.1
self.w = np.random.rand(self.dimensions, 1)
self.b = np.random.rand(1)
def query_data(self, **kwargs):
"""
Once initialized, this method will create more data.
Args:
samples: number of samples of data needed (optional, default randomly 10k - 50k)
Returns:
tuple: data a tuple, ``(x,y)``
``x`` is a two or one dimensional ndarray ordered such that axis 0 is independent
data and data is spread along axis 1.
``y`` is a 1D ndarray it will be of the same length as axis 0 or x.
"""
if 'samples' in kwargs.keys():
samples = kwargs['samples']
else:
samples = np.random.randint(low=1000, high=5000)
x = np.random.uniform(size=(samples, self.dimensions))
y = np.dot(x, self.w) + np.random.normal(self.mu, self.sigma, (samples, 1)) + self.b
return (x, y)
if __name__ == '__main__':
dg = dataset_generator() # Initialize a dataset creator
data_train = dg.query_data(samples=5000) # Create a random training dataset.
r = regressor(data_train) # This call should return a regressor object that is fully trained.
params = r.get_params() # This call should reaturn parameters of the model that are
# fully trained.
data_test = dg.query_data(samples=5000) # Create a random testing dataset.
predictions = r.get_predictions(data_test[0]) # This call should return predictions.
print( "Rmse error of predictions = " + str(rmse(data_test[1], predictions)) )
|
WenboTien/Machine_Learning_prac
|
project1/tiny1/test_script.py
|
Python
|
mit
| 3,231
|
[
"Gaussian"
] |
d21436b48a1a3374c9dd6d69b2015a03819ca54f3be02ce2b8cd2408c3854de2
|
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMulttest(RPackage):
"""Resampling-based multiple hypothesis testing"""
homepage = "https://www.bioconductor.org/packages/multtest/"
url = "https://git.bioconductor.org/packages/multtest"
version('2.32.0', git='https://git.bioconductor.org/packages/multtest', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
depends_on('r@3.4.0:3.4.9', when='@2.32.0')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
|
lgarren/spack
|
var/spack/repos/builtin/packages/r-multtest/package.py
|
Python
|
lgpl-2.1
| 1,752
|
[
"Bioconductor"
] |
8d971809999cb7af74bef9f05dc66fddbb4cd27735f71ac8c087554df27aed98
|
""" EmailAgent
This agent reads the ResourceStatusCache table of ResourceStatusDB
for sending emails with aggregated information about state changes,
and then clears it.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN EmailAgent
:end-before: ##END
:dedent: 2
:caption: EmailAgent options
"""
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ResourceStatusSystem.Client.ResourceStatusClient import ResourceStatusClient
from DIRAC.ResourceStatusSystem.Utilities import RssConfiguration
from DIRAC.Interfaces.API.DiracAdmin import DiracAdmin
AGENT_NAME = "ResourceStatus/EmailAgent"
class EmailAgent(AgentModule):
def __init__(self, *args, **kwargs):
AgentModule.__init__(self, *args, **kwargs)
self.diracAdmin = None
self.default_value = None
self.rsClient = ResourceStatusClient()
def initialize(self, *args, **kwargs):
"""EmailAgent initialization"""
self.diracAdmin = DiracAdmin()
return S_OK()
@staticmethod
def _groupBySiteName(result):
"""
Group results by SiteName
"""
siteNameCol = result["Columns"].index("SiteName")
resultValue = result["Value"]
siteNameDict = {}
for row in resultValue:
if row[siteNameCol] not in siteNameDict:
siteNameDict[row[siteNameCol]] = [row]
else:
siteNameDict[row[siteNameCol]].append(row)
return siteNameDict
def execute(self):
result = self.rsClient.select("ResourceStatusCache")
if not result["OK"]:
return S_ERROR()
columnNames = result["Columns"]
result = self._groupBySiteName(result)
for site, records in result.items():
email = ""
html_body = ""
html_elements = ""
if gConfig.getValue("/DIRAC/Setup"):
setup = "(" + gConfig.getValue("/DIRAC/Setup") + ")\n\n"
else:
setup = ""
html_header = """\
<!DOCTYPE html>
<html>
<head>
<meta charset='UTF-8'>
<style>
table{{color:#333;font-family:Helvetica,Arial,sans-serif;min-width:700px;border-collapse:collapse;border-spacing:0}}
td,th{{border:1px solid transparent;height:30px;transition:all .3s}}th{{background:#DFDFDF;font-weight:700}}
td{{background:#FAFAFA;text-align:center}}.setup{{font-size:150%;color:grey}}.Banned{{color:red}}.Error{{color:#8b0000}}
.Degraded{{color:gray}}.Probing{{color:#00f}}.Active{{color:green}}tr:nth-child(even)
td{{background:#F1F1F1}}tr:nth-child(odd)
td{{background:#FEFEFE}}tr td:hover{{background:#666;color:#FFF}}
</style>
</head>
<body>
<p class="setup">{setup}</p>
""".format(
setup=setup
)
for row in records:
statusType = row[columnNames.index("StatusType")]
resourceName = row[columnNames.index("ResourceName")]
status = row[columnNames.index("Status")]
time = row[columnNames.index("Time")]
previousStatus = row[columnNames.index("PreviousStatus")]
html_elements += (
"<tr>"
+ "<td>"
+ statusType
+ "</td>"
+ "<td>"
+ resourceName
+ "</td>"
+ "<td class='"
+ status
+ "'>"
+ status
+ "</td>"
+ "<td>"
+ str(time)
+ "</td>"
+ "<td class='"
+ previousStatus
+ "'>"
+ previousStatus
+ "</td>"
+ "</tr>"
)
html_body = """\
<table>
<tr>
<th>Status Type</th>
<th>Resource Name</th>
<th>Status</th>
<th>Time</th>
<th>Previous Status</th>
</tr>
{html_elements}
</table>
</body>
</html>
""".format(
html_elements=html_elements
)
email = html_header + html_body
subject = "RSS actions taken for " + str(site) + "\n"
self._sendMail(subject, email, html=True)
self.rsClient.delete("ResourceStatusCache")
return S_OK()
def _sendMail(self, subject, body, html=False):
userEmails = self._getUserEmails()
if not userEmails["OK"]:
return userEmails
# User email address used to send the emails from.
fromAddress = RssConfiguration.RssConfiguration().getConfigFromAddress()
for user in userEmails["Value"]:
# FIXME: should not I get the info from the RSS User cache ?
resEmail = self.diracAdmin.sendMail(user, subject, body, fromAddress=fromAddress, html=html)
if not resEmail["OK"]:
return S_ERROR('Cannot send email to user "%s"' % user)
return S_OK()
def _getUserEmails(self):
configResult = RssConfiguration.getnotificationGroups()
if not configResult["OK"]:
return configResult
try:
notificationGroups = configResult["Value"]["notificationGroups"]
except KeyError:
return S_ERROR("%s/notificationGroups not found")
notifications = RssConfiguration.getNotifications()
if not notifications["OK"]:
return notifications
notifications = notifications["Value"]
userEmails = []
for notificationGroupName in notificationGroups:
try:
userEmails.extend(notifications[notificationGroupName]["users"])
except KeyError:
self.log.error("%s not present" % notificationGroupName)
return S_OK(userEmails)
|
ic-hep/DIRAC
|
src/DIRAC/ResourceStatusSystem/Agent/EmailAgent.py
|
Python
|
gpl-3.0
| 6,111
|
[
"DIRAC"
] |
db77c47c1e907cd8363f581eb1d59baf33fe872533ed611b2b710b383b86524d
|
#!/usr/bin/env python
# 26.09.2006, c
import os.path as op
from optparse import OptionParser
import init_sfepy
from sfepy.base.base import *
from sfepy.fem.mesh import Mesh
from sfepy.fem.meshio import HDF5MeshIO
from sfepy.solvers.ts import TimeStepper
from sfepy.base.ioutils import get_trunk, write_dict_hdf5
##
# c: 26.09.2006, r: 09.07.2008
def dump_to_vtk( filename, options, steps = None ):
output( 'dumping to VTK...' )
mesh = Mesh.from_file( filename )
io = HDF5MeshIO( filename )
ts = TimeStepper( *io.read_time_stepper() )
if options.output_filename_trunk:
ofn_trunk = options.output_filename_trunk
else:
ofn_trunk = get_trunk( filename )
if steps is None:
iterator = ts.iter_from( options.step0 )
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output( ts.format % (step, ts.n_step - 1) )
out = io.read_data( step )
if out is None: break
mesh.write( ofn_trunk + ts.suffix % step + '.vtk',
io = 'auto', out = out )
output( '...done' )
return ts.suffix
##
# c: 26.09.2006, r: 23.06.2008
def extract_time_history( filename, options ):
output( 'extracting selected data...' )
el = options.extract_list
output( 'extraction list:', el )
##
# Parse extractions.
pes = OneTypeList( Struct )
for chunk in el.split( ',' ):
aux = chunk.strip().split()
pes.append( Struct( var = aux[0],
mode = aux[1],
indx = map( int, aux[2:] ),
igs = None ) )
##
# Verify array limits, set igs for element data, shift indx.
mesh = Mesh.from_file( filename )
n_el, n_els, offs = mesh.n_el, mesh.n_els, mesh.el_offsets
for pe in pes:
if pe.mode == 'n':
for ii in pe.indx:
if (ii < 0) or (ii >= mesh.n_nod):
raise IndexError, 'node index 0 <= %d < %d'\
% (ii, mesh.n_nod)
if pe.mode == 'e':
pe.igs = []
for ii, ie in enumerate( pe.indx[:] ):
if (ie < 0) or (ie >= n_el):
raise IndexError, 'element index 0 <= %d < %d'\
% (ie, n_el)
ig = (ie < n_els).argmax()
pe.igs.append( ig )
pe.indx[ii] = ie - offs[ig]
## print pes
##
# Extract data.
# Assumes only one element group (ignores igs)!
io = HDF5MeshIO( filename )
ths = {}
for pe in pes:
mode, nname = io.read_data_header( pe.var )
print mode, nname
if ((pe.mode == 'n' and mode == 'vertex') or
(pe.mode == 'e' and mode == 'cell')):
th = io.read_time_history( nname, pe.indx )
elif pe.mode == 'e' and mode == 'vertex':
conn = mesh.conns[0]
th = {}
for iel in pe.indx:
ips = conn[iel]
th[iel] = io.read_time_history( nname, ips )
else:
raise RuntimeError, 'cannot extract cell data %s in nodes' % pe.var
ths[pe.var] = th
return ths
##
# 27.09.2006, c
def average_vertex_var_in_cells( ths_in ):
ths = dict.fromkeys( ths_in.keys() )
for var, th in ths_in.iteritems():
aux = dict.fromkeys( th.keys() )
for ir, data in th.iteritems():
if isinstance( data, dict ):
for ic, ndata in data.iteritems():
if aux[ir] is None:
aux[ir] = ndata
else:
aux[ir] += ndata
aux[ir] /= float( len( data ) )
else:
aux[ir] = data
ths[var] = aux
return ths
usage = """%prog [options] filename_in"""
help = {
'filename' :
'basename of output file(s) [default: <basename of input file>]',
'dump' :
'dump to sequence of VTK files',
'from' :
'start dumping from step ii [default: %default]',
'extract' :
'extract variables according to extraction list',
'average' :
'average vertex variable into cells ("e" extraction mode)'
}
##
# c: 26.09.2006, r: 23.06.2008
def main():
version = open( op.join( init_sfepy.install_dir,
'VERSION' ) ).readlines()[0][:-1]
parser = OptionParser( usage = usage, version = "%prog " + version )
parser.add_option( "-o", "", metavar = 'filename',
action = "store", dest = "output_filename_trunk",
default = None, help = help['filename'] )
parser.add_option( "-d", "--dump",
action = "store_true", dest = "dump",
default = False, help = help['dump'] )
parser.add_option( "-f", "--from", type = int, metavar = 'ii',
action = "store", dest = "step0",
default = 0, help = help['from'] )
parser.add_option( "-e", "--extract", metavar = 'list',
action = "store", dest = "extract_list",
default = None, help = help['extract'] )
parser.add_option( "-a", "--average",
action = "store_true", dest = "average",
default = False, help = help['average'] )
(options, args) = parser.parse_args()
print options
print args
if (len( args ) == 1):
filename_in = args[0];
else:
parser.print_help(),
return
if options.dump:
dump_to_vtk( filename_in, options )
if options.extract_list:
ths = extract_time_history( filename_in, options )
## print ths
if options.average:
ths = average_vertex_var_in_cells( ths )
## print ths
if options.output_filename_trunk:
ts = TimeStepper( *HDF5MeshIO( filename_in ).read_time_stepper() )
ths.update( {'times' : ts.times, 'dt' : ts.dt} )
write_dict_hdf5( options.output_filename_trunk + '.h5', ths )
if __name__ == '__main__':
main()
|
certik/sfepy
|
extractor.py
|
Python
|
bsd-3-clause
| 6,130
|
[
"VTK"
] |
ce41e16596bc4c66d6557a9cc34c4bc9d64aafc615ea8659a7849d764f5e998b
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
hmn = pylid.PyLID(3)
hmn.total_ngrams = 159771623
hmn.lang = 'hmn'
hmn.ngrams = Counter({
u' ts': 1396157,
u'ab ': 1298229,
u'as ': 1253541,
u'is ': 1205135,
u's t': 1203015,
u'aj ': 1159263,
u'og ': 1127684,
u'us ': 1035520,
u'b t': 1030888,
u' th': 1003773,
u'av ': 986135,
u'au ': 964010,
u'ob ': 955519,
u'ov ': 907683,
u' nt': 893941,
u'oj ': 879095,
u'ej ': 865846,
u'v t': 857682,
u'wm ': 833756,
u' ta': 830449,
u' tu': 817529,
u' mu': 813789,
u'ub ': 811586,
u' la': 785645,
u' ha': 755660,
u' tx': 754911,
u'ua ': 731924,
u'tsi': 725217,
u'awm': 697784,
u'ag ': 696521,
u'j t': 692586,
u'os ': 683567,
u'am ': 676016,
u'hia': 657793,
u' li': 647039,
u'eb ': 644215,
u' yo': 638917,
u' ko': 634405,
u'ib ': 628171,
u'law': 625215,
u' no': 609098,
u'uv ': 602894,
u' co': 600941,
u'es ': 596190,
u'wb ': 590504,
u'm t': 587908,
u's n': 587382,
u'uav': 587261,
u' ua': 586168,
u'oob': 582898,
u'li ': 581803,
u'g t': 578955,
u' lo': 576531,
u'sis': 572789,
u'yog': 571650,
u'b n': 564906,
u'uaj': 562123,
u'thi': 561394,
u'iab': 558066,
u' yu': 557361,
u' lu': 552179,
u'hai': 542841,
u'tau': 537182,
u' ti': 536965,
u'wv ': 530969,
u'yua': 511170,
u'mua': 501126,
u'los': 497148,
u'om ': 496363,
u'ais': 490419,
u'eej': 473849,
u's y': 472353,
u' ku': 467284,
u'no ': 463703,
u'v n': 459355,
u'ws ': 447585,
u'moo': 441604,
u' ra': 440335,
u' ne': 437929,
u's l': 434720,
u'm n': 418757,
u' si': 417635,
u'rau': 416356,
u'wg ': 411708,
u' ny': 411316,
u'awv': 407445,
u'g l': 401684,
u'tia': 401435,
u'koj': 399616,
u'nta': 399242,
u'ug ': 397908,
u'im ': 392615,
u's k': 382902,
u'b l': 382547,
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u' ce': 379238,
u'j n': 379026,
u' ma': 376349,
u' te': 373592,
u'kuv': 372913,
u'hau': 366346,
u'em ': 363120,
u'ev ': 363090,
u'um ': 358613,
u'tse': 350411,
u'taw': 347144,
u'g n': 346486,
u' pe': 345955,
u'uas': 344402,
u' pa': 327854,
u'ces': 315720,
u' xw': 313880,
u'mus': 313320,
u'ias': 312711,
u'tua': 312451,
u'j l': 306704,
u'v l': 306171,
u'eg ': 304172,
u'lub': 303993,
u'tus': 299013,
u'b c': 298299,
u'Hmo': 297674,
u'oo ': 296353,
u'xwb': 291300,
u's m': 289213,
u'm l': 282739,
u'aum': 282306,
u' ib': 280979,
u' Hm': 280653,
u' ca': 276218,
u's p': 272738,
u'eem': 270685,
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u' tw': 264181,
u'iaj': 263394,
u'tha': 262964,
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u'peb': 261413,
u' zo': 259666,
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u'see': 257845,
u'eeg': 255613,
u' qh': 252248,
u'uj ': 251959,
u'nee': 251004,
u'mas': 250936,
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u'yee': 238741,
u'ng ': 234351,
u'b m': 233135,
u'hov': 231992,
u'aub': 229683,
u'b y': 229281,
u' po': 228375,
u'b k': 225849,
u' ya': 225066,
u' ye': 222642,
u'awg': 222199,
u'txo': 221281,
u'si ': 221037,
u'zoo': 220097,
u'txh': 219327,
u' nw': 218390,
u' le': 216378,
u'v m': 216102,
u'nyo': 215917,
u'j h': 213162,
u' da': 210822,
u'iag': 209473,
u' ka': 208930,
u'tsh': 207499,
u'j y': 206599,
u'a t': 203345,
u'pau': 203254,
u'g k': 202720,
u' nr': 201384,
u'yob': 199625,
u'v k': 198220,
u' xa': 197844,
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u'b p': 195454,
u's h': 192589,
u'o t': 192199,
u'aws': 192046,
u's c': 191794,
u'j m': 189189,
u'txi': 188147,
u' ke': 187206,
u'j k': 184753,
u'm k': 181769,
u'lua': 180486,
u'b s': 179686,
u'v h': 178966,
u'j c': 177279,
u' me': 175555,
u'v p': 172139,
u'txa': 171953,
u' na': 171459,
u'v y': 171457,
u'haw': 170786,
u' pu': 168793,
u'i n': 168537,
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|
dmort27/pylid
|
pylid/langs/hmn.py
|
Python
|
mit
| 773,284
|
[
"ASE",
"BWA",
"CDK",
"EPW",
"Elk",
"MOE",
"VMD"
] |
9d5eeffe6a0d07a02022447797e0e5d6c3eb3644ee8a21791b3a28b0eb2e0f70
|
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2012 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id$
#-------------------------------------------------------------------------
#
# Standard Python Modules
#
#-------------------------------------------------------------------------
import logging
LOG = logging.getLogger(".Db")
#-------------------------------------------------------------------------
#
# Gramps Modules
#
#-------------------------------------------------------------------------
#-------------------------------------------------------------------------
#
# Constants
#
#-------------------------------------------------------------------------
_MINVERSION = 9
_DBVERSION = 14
#-------------------------------------------------------------------------
#
# Importing data into the currently open database.
# Ability to import .grdb files removed in accordance with
# http://gramps.1791082.n4.nabble.com/Status-of-GEPS-023-tp4329141p4329746.html
#
#-------------------------------------------------------------------------
def importData(database, filename, user):
user.notify_error(_("%s could not be opened") % filename,
_("The Database version is not supported "
"by this version of Gramps."
"You should use an old copy of Gramps at "
"version 3.0.x and import your database into "
"that version. You should then export a copy "
"of your data to Gramps XML (family tree). "
"Then you should upgrade to the latest "
"version of Gramps (for example this version), "
"create a new empty database and import the "
"Gramps XML into that version. "
"Please refer to:"
"http://www.gramps-project.org/wiki/index.php?"
"title=Gramps_3.4_Wiki_Manual_-_Manage_Family_Trees#"
"Moving_a_Gramps_2.2_databases_to_Gramps_3.x"))
return
|
arunkgupta/gramps
|
gramps/plugins/import/importgrdb.py
|
Python
|
gpl-2.0
| 2,858
|
[
"Brian"
] |
b24bd994a044c8b10943bd5d08db89456e50c493ca3b06a18c1b88e50885871c
|
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
"""This module contains a collection of printing functions for this package."""
import numpy as np
import sys
TAB = " " * 2
def print_complex(np_complex, scaling=1.0, precision=6):
"""Return a string of a (numpy) complex number."""
freq_f = "{{0:> {},.{}f}}".format(7 + precision, precision)
if np_complex.imag:
# the first case should not be possible...
if np_complex.real:
pm = "+-"[np_complex.imag < 0.0]
return (freq_f + pm + freq_f + "i").format(np_complex.real,
abs(np_complex.imag))
else:
return (freq_f + "i").format(np_complex.imag)
else:
return (freq_f + " ").format(np_complex.real * scaling)
def print_harmonics(harmonic, scaling=1.0,):
"""Return an output string containing harmonic frequencies in 1/cm."""
output_string = "Harmonic vibrational properties\n"
output_string += " i v [1/cm]"
harm_frequencies = harmonic.freq_inv_cm
nTransRot = harmonic.geometry.nTransRot()
if np.any(harmonic.dipole_derivatives):
output_string += " " * 4 + "I [km/mol]\n" + "-" * 28 + "\n"
tmp_str = '{0:> 4,d} {1} {2:>10,.4f}\n'
harm_intensities = harmonic.harmonic_intensities()
for i, f in enumerate(harm_frequencies):
if i == nTransRot:
output_string += " " + "-" * 25 + "\n"
output_string += tmp_str.format(i + 1,
print_complex(f, scaling, 4),
harm_intensities[i])
output_string += "-" * 28 + "\n"
else:
output_string += "\n" + "-" * 17 + "\n"
tmp_str = '{0:> 4,d} {1}\n'
for i, f in enumerate(harm_frequencies):
if i == nTransRot:
output_string += " " + "-" * 13 + "\n"
output_string += tmp_str.format(i + 1,
print_complex(f, scaling, 4))
output_string += "-" * 17 + "\n"
return output_string
def csv_harmonics(harmonic, scaling=1.0,):
"""Return a comma-separated-value string of the harmonic transitions."""
output_string = ""
if not np.any(harmonic.dipole_derivatives):
sys.exit("Printfunctons.csv_harmonics():" +
"Dipole derivatives are required to produce a 2D csv.")
nTransRot = harmonic.geometry.nTransRot()
frequencies = harmonic.freq_inv_cm[nTransRot:].real
intensities = harmonic.harmonic_intensities()[nTransRot:]
csv_str = "{:> 9.3f}, {:> 10.4f}\n"
for i in range(harmonic.geometry.nVib()):
output_string += csv_str.format(frequencies[i] * scaling,
intensities[i])
return output_string
def print_np_2Dmatrix(mat, precision=9):
"""Pretty print a 2D-matrix."""
output_string = "" # + TAB
shape = mat.shape
if not len(shape) == 2:
return "Matrix not two-dimensional"
for line in mat:
for element in line:
element = np.complex(element)
output_string += print_complex(element, 1.0, precision) # + TAB
output_string += "\n" # + TAB
return output_string # [:-len(TAB)]
def print_VibRot_constants(alpha, geometry, precision=8):
"""Print the Vibrational-rotational constants alpha_k."""
nVib, nTransRot = geometry.nVib(), geometry.nTransRot()
output_string = "Vibrational-Rotational constants:\n\n"
const_str = " {{:> {},.{}f}}".format(6 + precision, precision)
for a in range(3):
for i in range(nVib):
j = i + nTransRot + 1
v = alpha[a, i]
output_string += ("{:> 3,d} " * 2).format(a + 1, j)
output_string += (const_str * 4).format(*v)
output_string += const_str.format(np.sum(v)) + '\n'
return output_string
def print_rigid_rotational_constants(rotation, model='rigid'):
"""Print rotational constants in cm^-1 and MHz."""
output_string = "{} rotational constants (".format(model.title())
if model == 'rigid':
abc_e_M = rotation.rigid_rotational_constants("MHz")
abc_e_c = rotation.rigid_rotational_constants("1/cm")
r_type = rotation.geometry.rot_prop.rotational_symmetry()[1]
output_string += "{} molecule)\n".format(r_type.title())
output_string += ' {:^12} {:^12}\n'.format('1/cm', 'MHz')
for i, l in enumerate(['A', 'B', 'C']):
if abc_e_c[i] > 1e-5:
output_string += '{} '.format(l)
output_string += '{:> 12,.6f} '.format(abc_e_c[i])
output_string += '{:> 12,.2f} \n'.format(abc_e_M[i])
return output_string
else:
sys.exit("PrintFunctions.print_rigid_rotational_constants(): "
"Model {} is undefined.".format(model))
def print_anharmonic_constants(chi, precision=6):
"""Print the anharmonic constants chi."""
output_string = "Anharmonic constants:\n\n"
const_str = " {{:> {},.{}f}}\n".format(7 + precision, precision)
# print_str = "{:> 3,d} " + const_str * self.geometry.nVib() + '\n'
for i, row in enumerate(chi):
i += 7
for j, value in enumerate(row):
j += 7
if j >= i:
output_string += ("{:> 3,d} {:> 3,d}" +
const_str).format(i, j, value)
# output_string += print_str.format(i, *row)
return output_string
def print_coriolis_zeta(coriolis_zeta, precision=6):
"""Print the Coriolis zeta matrices."""
output_string = ""
const_str = " {{:> {},.{}f}}".format(7 + precision, precision)
print_str = "{:> 3,d} " * 2 + const_str * 3 + '\n'
threeN = len(coriolis_zeta[0])
for i in range(threeN):
for j in range(threeN):
if (i != j and i > j):
output_string += print_str.format(i + 1, j + 1,
coriolis_zeta[0, i, j],
coriolis_zeta[1, i, j],
coriolis_zeta[2, i, j])
return output_string
def print_force_constants(fc_mat, geometry,
mat_type="cubic", precision=4):
"""
Return an output string of a pretty printed force constant matrix.
mat_type: ("quadratic", "cubic", "semi-quartic")
"""
output_string = ""
nVib, nTransRot = geometry.nVib(), geometry.nTransRot()
const_str = " {{:> {},.{}f}}".format(7 + precision, precision)
corr = nTransRot + 1 # correction for printing
print_zero = False
if mat_type == "quadratic":
print_str = "{:> 3,d} " + const_str + '\n'
for i in range(nVib):
output_string += print_str.format(i + 1, fc_mat[i + nTransRot,
i + nTransRot])
elif mat_type == "cubic":
print_str = "{:> 3,d} " * 3 + const_str + '\n'
for i in range(nVib):
for j in range(nVib):
for k in range(nVib):
if (np.abs(fc_mat[i, j, k]) < 1e-4 and not print_zero):
continue
output_string += print_str.format(i + corr,
j + corr,
k + corr,
fc_mat[i, j, k])
elif mat_type == "semi-quartic":
print_str = "{:> 3,d} " * 4 + const_str + '\n'
for i in range(nVib):
for j in range(nVib):
for k in range(nVib):
if np.abs(fc_mat[i, j, k]) < 1e-4:
continue
output_string += print_str.format(i + corr,
j + corr,
k + corr,
k + corr,
fc_mat[i, j, k])
else:
sys.exit("PrintFunctions.print_force_constants(): "
"mat_type \'{}\' unknown".format(mat_type))
return output_string
def print_cartesian_diplacements(harmonic, unit="bohr",
precision=9, scaling=1.0):
"""
Return a string of back transformed normal coordinates.
Unit: Bohr or Angstroem.
This method should produce the same numbers as in the cfour QUADRATURE
file (in bohr).
"""
output_string = ""
vec_str = " {{:> {},.{}f}}".format(5 + precision, precision)
freq_str = "{}\nv{} = {} 1/cm\n"
inten_str = "{}\nv_{} = {} 1/cm, I_{} = {:,.3f} km/mol\n"
nAtoms = harmonic.geometry.nAtoms
nTransRot = harmonic.geometry.nTransRot()
harm_inv_cm = harmonic.freq_inv_cm[nTransRot:]
if np.all(harmonic.dipole_derivatives):
intensities = harmonic.harmonic_intensities()[nTransRot:]
cart_disps = harmonic.cartesian_displacements(1.0, unit)[0]
for i, disp in enumerate(cart_disps):
freq = print_complex(harm_inv_cm[i], scaling, 2)
if np.all(harmonic.dipole_derivatives):
output_string += inten_str.format(nAtoms, i + 1, freq,
i + 1, intensities[i])
else:
output_string += freq_str.format(nAtoms, i + 1, freq)
for a, atom in enumerate(harmonic.geometry.atoms):
v = np.zeros((3,))
for j in range(3):
v[j] = disp[3 * a + j]
# atom.coordinates are given in Angstroem
output_string += atom.print_cartesian(precision, unit) + " "
output_string += (vec_str * 3).format(*v) + "\n"
return output_string
def print_normal_coordinates(normal_modes, nTransRot=6):
"""Return an output string containing the normal coordinates."""
sFormat_Vib = "{:>8,.5f} " * (len(normal_modes) - nTransRot) + '\n'
output_string = 'Translational and Rotational modes:\n'
for normal_mode in normal_modes:
string = ""
for p in normal_mode[:nTransRot]:
string += "{0:>6,.3f}{1}{2:>5,.3f}j ".format(p.real,
'+-'[p.imag < 0],
abs(p.imag))
output_string += string + '\n'
output_string += '\nVibrational modes:\n'
for normal_mode in normal_modes:
output_string += sFormat_Vib.format(
*[f.real for f in normal_mode[nTransRot:]])
print(output_string)
def print_harmonic_VPT2_derivatives(vpt2_derivatives, harmonic, precision=3):
"""
Print Matthew's harmonic VPT2 derivative matrix.
This matrix can indicate the presence of Fermi resonances.
"""
emph = '\033[91m' # '\033[1m' - bold, '\033[91m' - red, '\033[4m' - uline
value_str = " {{:> {},.{}f}}".format(4 + precision, precision)
emph_value_str = emph + value_str + '\033[0m'
output_string = "\nHarmonic VPT2 derivative matrix:\n\n"
nVib = harmonic.geometry.nVib()
header = (" " * precision + "v_{:<3,d}") * nVib
output_string += " " * 5 + header.format(*list(range(1, nVib + 1))) + '\n'
for i in range(nVib):
output_string += "w_{:<3,d}".format(i + 1)
for j in range(nVib):
value = vpt2_derivatives[i, j]
if abs(value) >= 0.5:
output_string += emph_value_str.format(value)
else:
output_string += value_str.format(value)
output_string += "\n"
return output_string
def print_optimisation_sumary(energies, shorten=False, precision=9):
"""Print all energies in nice column."""
e_str = "{{:.{}f}}".format(precision)
mapping = {"E_SCF": ["E[SCF]/Eh", e_str],
"E_MP2": ["E[MP2]/Eh", e_str],
"E_CCSD": ["E[CCSD]/Eh", e_str],
"E_(T)": ["E[(T)]/Eh", e_str],
"total": ["E[tot]/Eh", e_str],
"log_diff": ["–lg|ΔE|", "{:.2f}"],
"grad_norm": ["|Grad|/a.u.", "{:.4e}"]}
# Table
last_iter = max(energies)
keys = list(energies[0].keys())
nkeys = len(keys)
iterations = list(range(last_iter + 1))
if (shorten and last_iter > 6):
iterations = [0, 1, 2, last_iter - 3, last_iter - 2, last_iter - 1]
table_data = []
max_str_size = [len(mapping[k][0]) for k in keys]
for i in iterations:
iter_data = [str(i + 1)]
if (shorten and last_iter > 6 and i == last_iter - 3):
table_data.append(["⋮"] + ["⋮ " for k in keys])
for j, k in enumerate(keys):
if k in energies[i]:
formated_str = mapping[k][1].format(energies[i][k])
iter_data.append(formated_str)
max_str_size[j] = max(max_str_size[j], len(formated_str))
else:
iter_data.append("– ")
table_data.append(iter_data)
table_str = "{{:>{}}} " * nkeys
table_str = "{:>4} " + table_str.format(*max_str_size) + "\n"
table = ""
for iteration in table_data:
table += table_str.format(*iteration)
# Header
header_names = [mapping[k][0] for k in keys]
header_str = "{{:^{}}} " * nkeys
header_str = "Iter " + header_str.format(*max_str_size)
header = header_str[:-1].format(*header_names) + "\n"
hline = "—" * len(header) + "\n"
header += hline
return header + table + hline
|
jdcapa/MolecularToolbox
|
moleculartoolbox/printfunctions.py
|
Python
|
gpl-3.0
| 13,523
|
[
"CFOUR"
] |
ef807e5a1ab090999fdae3f88d88816521ace479a5fe1a0a82a0e80ca15b629f
|
"""
Double ring model
References:
Ardid, Wang, Compte 2007 Journal of Neuroscience
doi: 10.1523/JNEUROSCI.1145-07.2007
How is the long-range connection modeled?
"""
from __future__ import division
from collections import OrderedDict
from scipy.signal import fftconvolve
import scipy.stats
import random as pyrand # Import before Brian floods the namespace
# Once your code is working, turn units off for speed
# import brian_no_units
from brian import *
# Notice scipy.fftpack.rfft behaves differently from numpy.fft.rfft
from numpy.fft import rfft, irfft
# Make Brian faster
set_global_preferences(
useweave=True,
usecodegen=True,
usecodegenweave=True,
usecodegenstateupdate=True,
usenewpropagate=True,
usecodegenthreshold=True,
gcc_options=['-ffast-math', '-march=native']
)
#=========================================================================================
# Helper function
#=========================================================================================
def angle_diff(theta1, theta2, mode='rad'):
# Compute the angle difference between theta1 and theta2 on a circle
angle_circle = 2*np.pi if mode == 'rad' else 360.
diff = abs(theta1-theta2)
return np.minimum(diff, angle_circle-diff)
#=========================================================================================
# Equations
#=========================================================================================
equations = dict(
E = '''
dV/dt = (-(V - V_L) + Isyn/gE) / tau_m_E : mV
dsAMPA/dt = -sAMPA/tauAMPA : 1
dx/dt = -x/tau_x : 1
dsNMDA/dt = -sNMDA/tauNMDA + alpha*x*(1 - sNMDA) : 1
Isyn = I_AMPA_ext + I_AMPA + I_NMDA + I_GABA + Istim : pA
I_AMPA_ext = -G_AMPA_ext*(V - V_E) : pA
I_AMPA = -G_AMPA*(V - V_E) : pA
I_NMDA = -G_NMDA*(V - V_E)/(1 + exp(-a*V)/b) : pA
I_GABA = -G_GABA*(V - V_I) : pA
dG_AMPA_ext/dt= -G_AMPA_ext/tauAMPA : nS
G_AMPA : nS
G_NMDA : nS
G_GABA : nS
Istim : pA
''',
I = '''
dV/dt = (-(V - V_L) + Isyn/gI) / tau_m_I : mV
dsGABA/dt = -sGABA/tauGABA : 1
Isyn = I_AMPA_ext + I_AMPA + I_NMDA + I_GABA : pA
I_AMPA_ext = -G_AMPA_ext*(V - V_E) : pA
I_AMPA = -G_AMPA*(V - V_E) : pA
I_NMDA = -G_NMDA*(V - V_E)/(1 + exp(-a*V)/b) : pA
I_GABA = -G_GABA*(V - V_I) : pA
dG_AMPA_ext/dt= -G_AMPA_ext/tauAMPA : nS
G_AMPA: nS
G_NMDA: nS
G_GABA: nS
'''
)
#=========================================================================================
# Model Parameters
#=========================================================================================
modelparams = dict()
modelparams['neuron'] = dict(
# Number of neurons
N_E = 1024,
N_I = 256,
# Common LIF
V_L = -70*mV,
Vth = -50*mV,
Vreset = -60*mV,
# Excitatory LIF
gE = 25*nS,
tau_m_E = 20*ms,
tau_ref_E = 2*ms,
# Inhibitory LIF
gI = 20*nS,
tau_m_I = 10*ms,
tau_ref_I = 1*ms,
# Reversal potentials
V_E = 0*mV,
V_I = -70*mV,
# NMDA nonlinearity
a = 0.062*mV**-1,
b = 3.57,
# Synaptic time constants
tauAMPA = 2*ms,
tau_x = 2*ms,
tauNMDA = 100*ms,
alpha = 0.5*kHz,
tauGABA = 10*ms,
# Background noise
nu_ext = 1.8*kHz
)
modelparams['mt'] = dict(
# recurrent connectivity footprint
sigma_EE = 14.4,
JEE_plus = 1.62,
# Unscaled recurrent synaptic conductances (onto excitatory)
gAMPA_E = 0.005*1024*nS,
gNMDA_E = 0.093*1024*nS,
gGABA_E = 1.47*256*nS,
# Unscaled recurrent synaptic conductances (onto inhibitory)
gAMPA_I = 0.005*1024*nS,
gNMDA_I = 0.195*1024*nS,
gGABA_I = 0.391*256*nS,
# External synaptic conductances
gAMPA_ext_E = 15.0*nS,
gAMPA_ext_I = 4.5*nS,
)
modelparams['pfc'] = dict(
# recurrent connectivity footprint
sigma_EE = 14.4,
JEE_plus = 1.62,
# Unscaled recurrent synaptic conductances (onto excitatory)
gAMPA_E = 0.391*1024*nS,
gNMDA_E = 0.732*1024*nS,
gGABA_E = 3.74*256*nS,
# Unscaled recurrent synaptic conductances (onto inhibitory)
gAMPA_I = 0.293*1024*nS,
gNMDA_I = 0.566*1024*nS,
gGABA_I = 2.87*256*nS,
# External synaptic conductances
gAMPA_ext_E = 3.1*nS,
gAMPA_ext_I = 2.38*nS
)
modelparams['conn'] = dict(
# Connectivity footprint
sigma_mt2pfc = 36.,
sigma_pfc2mt = 72.,
# Unscaled long range synaptic conductances (onto excitatory)
gAMPA_E_mt2pfc = 0.005*1024*nS,
gAMPA_E_pfc2mt = 0.146*1024*nS,
# Unscaled long range synaptic conductances (onto inhibitory)
gAMPA_I_mt2pfc = 0*nS,
gAMPA_I_pfc2mt = 0.039*1024*nS
)
#=========================================================================================
# Stimulus Parameters
#=========================================================================================
stimparams = dict(
Ton = 500 * ms,
Toff = 750 * ms,
I0_E = 1. * nA,
I1_E = 0.9 * nA,
I0_I = 0.2 * nA,
I1_I = 0.18 * nA,
mu = 2.53,
theta_stim = 180,
Igate = 0.025 * nA
)
#=========================================================================================
# Model
#=========================================================================================
class Model(NetworkOperation):
def __init__(self, modelparams,
stimparams, dt=0.02*ms):
#---------------------------------------------------------------------------------
# Initialize
#---------------------------------------------------------------------------------
# Create clocks
clocks = OrderedDict()
clocks['main'] = Clock(dt)
clocks['nmda'] = Clock(dt*10) # NMDA update is less frequent
clocks['mons'] = Clock(1.0*ms)
#clocks['mons'] = Clock(dt)
super(Model, self).__init__(clock=clocks['main'])
#---------------------------------------------------------------------------------
# Complete the model specification
#---------------------------------------------------------------------------------
# Model parameters
p = modelparams.copy()
p_neuron = p['neuron']
areas = ['mt','pfc'] # areas
conns = ['pfc2mt','mt2pfc'] # connections
# Rescale conductances by number of neurons
for area in areas:
for conductance in ['gAMPA_E', 'gAMPA_I', 'gNMDA_E', 'gNMDA_I']:
p[area][conductance] /= p_neuron['N_E']
for conductance in ['gGABA_E', 'gGABA_I']:
p[area][conductance] /= p_neuron['N_I']
for conn in conns:
p['conn']['gAMPA_E_'+conn] /= p_neuron['N_E']
p['conn']['gAMPA_I_'+conn] /= p_neuron['N_E']
#---------------------------------------------------------------------------------
# Neuron populations
#---------------------------------------------------------------------------------
net = OrderedDict() # Network objects
exc = OrderedDict()
inh = OrderedDict()
# E/I populations
for pop in ['E', 'I']:
net[pop] = NeuronGroup(len(areas)*p_neuron['N_'+pop],
Equations(equations[pop], **p_neuron),
threshold=p_neuron['Vth'],
reset=p_neuron['Vreset'],
refractory=p_neuron['tau_ref_'+pop],
clock=clocks['main'],
order=1, freeze=True)
# Excitatory subpopulations
for area in areas:
exc[area] = net['E'].subgroup(p_neuron['N_E'])
inh[area] = net['I'].subgroup(p_neuron['N_I'])
#---------------------------------------------------------------------------------
# Background AMPA input (post-synaptic)
#---------------------------------------------------------------------------------
for area in areas:
for pop, target in zip(['E','I'], [exc,inh]):
net['pg'+area+pop] = PoissonGroup(p_neuron['N_'+pop], p_neuron['nu_ext'],
clock=clocks['main'])
net['ic'+area+pop] = IdentityConnection(net['pg'+area+pop], target[area], 'G_AMPA_ext',
weight=p[area]['gAMPA_ext_'+pop])
#---------------------------------------------------------------------------------
# Recurrent connections
#---------------------------------------------------------------------------------
# Presynaptic variables
net['icAMPA'] = IdentityConnection(net['E'], net['E'], 'sAMPA')
net['icNMDA'] = IdentityConnection(net['E'], net['E'], 'x')
net['icGABA'] = IdentityConnection(net['I'], net['I'], 'sGABA')
def get_fw(N, sigma, J_plus=None):
dtheta = 2*np.pi*np.minimum(np.arange(N),N-np.arange(N))/N
if J_plus is not None:
sigma = deg2rad(sigma)
tmp = (2*scipy.stats.norm.cdf(np.pi/sigma)-1)/np.sqrt(2*np.pi)*sigma
J_minus = (1-J_plus*tmp)/(1-tmp)
w = J_minus+((J_plus-J_minus)*np.exp(-dtheta**2/2./sigma**2))
else:
w = np.exp(-dtheta**2/2./sigma**2)/sigma/np.sqrt(2*np.pi)
return rfft(w)
# Recurrent NMDA connections
N_E = p_neuron['N_E']
self.fw = dict()
for area in areas:
self.fw[area] = get_fw(N_E, p[area]['sigma_EE'], p[area]['JEE_plus'])
p_conn = p['conn']
for conn in ['pfc2mt','mt2pfc']:
self.fw[conn] = get_fw(N_E, p_conn['sigma_'+conn])
# PFC, MT only have within area NMDA connections
@network_operation(when='start', clock=clocks['nmda'])
def recurrent_NMDA():
for area in areas:
fsNMDA = rfft(self.exc[area].sNMDA)
self.exc[area].G_NMDA = irfft(self.fw[area] * fsNMDA, N_E) * p[area]['gNMDA_E']
self.inh[area].G_NMDA = fsNMDA[0] * p[area]['gNMDA_I']
# Recurrent GABA connections
@network_operation(when='start', clock=clocks['main'])
def recurrent_GABA():
for area in areas:
S = self.inh[area].sGABA.sum()
self.exc[area].G_GABA = S * p[area]['gGABA_E']
self.inh[area].G_GABA = S * p[area]['gGABA_I']
# AMPA
@network_operation(when='start', clock=clocks['main'])
def recurrent_AMPA():
fsAMPA = dict()
for area in areas:
fsAMPA[area] = rfft(self.exc[area].sAMPA)
self.exc[area].G_AMPA = irfft(self.fw[area] * fsAMPA[area], N_E) * p[area]['gAMPA_E']
self.inh[area].G_AMPA = fsAMPA[area][0] * p[area]['gAMPA_I']
for conn in conns:
area_from, area_to = conn.split('2')
tmp = irfft(self.fw[conn] * fsAMPA[area_from], N_E)
self.exc[area_to].G_AMPA += p_conn['gAMPA_E_'+conn] * tmp
# slicing [3::4] start from index 3 and take one every 4 number
self.inh[area_to].G_AMPA += p_conn['gAMPA_I_'+conn] * tmp[3::4]
#---------------------------------------------------------------------------------
# Stimulus
#---------------------------------------------------------------------------------
clocks['stim'] = Clock(10*ms)
@network_operation(when='start', clock=clocks['stim'])
def stimulus(clock):
t = clock.t
if self.stimparams['Ton'] <= t < self.stimparams['Toff']:
self.exc['mt'].Istim = self.Istim['E']
self.inh['mt'].Istim = self.Istim['I']
self.exc['pfc'].Istim = self.stimparams['Igate']
self.inh['pfc'].Istim = self.stimparams['Igate']
else:
self.exc['mt'].Istim = 0
self.inh['mt'].Istim = 0
self.exc['pfc'].Istim = 0
self.inh['pfc'].Istim = 0
#---------------------------------------------------------------------------------
# Record spikes
#---------------------------------------------------------------------------------
mons = OrderedDict()
var_list = ['G_AMPA', 'G_NMDA', 'G_GABA', 'V', 'G_AMPA_ext',
'I_AMPA', 'I_NMDA', 'I_GABA', 'Isyn']
for pop in ['E', 'I']:
mons['spike'+pop] = SpikeMonitor(net[pop], record=True)
mons['pop'+pop] = PopulationRateMonitor(net[pop], bin=0.1)
for var in var_list:
mons[var+pop] = StateMonitor(net[pop], var, record=True, clock=clocks['mons'])
for pop, target in zip(['E','I'], [exc,inh]):
for area in areas:
mons['spike'+area+pop] = SpikeMonitor(target[area], record=True)
mons['pop'+area+pop] = PopulationRateMonitor(target[area], bin=0.1)
pop = 'E'
for var in ['x','sNMDA','Istim']:
mons[var+pop] = StateMonitor(net[pop], var, record=True, clock=clocks['mons'])
#---------------------------------------------------------------------------------
# Setup
#---------------------------------------------------------------------------------
self.p = p
self.stimparams = stimparams
self.net = net
self.exc = exc
self.inh = inh
self.mons = mons
self.clocks = clocks
# Add network objects and monitors to NetworkOperation's contained_objects
self.contained_objects += self.net.values() + self.mons.values()
self.contained_objects += [recurrent_GABA,recurrent_NMDA,recurrent_AMPA]
self.contained_objects += [stimulus]
def reinit(self, seed=123):
# Re-initialize random number generators
pyrand.seed(seed)
np.random.seed(seed)
# Reset network components, monitors, and clocks
for n in self.net.values() + self.mons.values() + self.clocks.values():
n.reinit()
# Randomly initialize membrane potentials
for pop in ['E', 'I']:
self.net[pop].V = np.random.uniform(self.p['neuron']['Vreset'],
self.p['neuron']['Vth'],
size=len(self.net[pop].V))
# Set synaptic variables to zero
for var in ['sAMPA', 'x', 'sNMDA']:
setattr(self.net['E'], var, 0)
for var in ['sGABA']:
setattr(self.net['I'], var, 0)
# Set stimulus
self.Istim = dict()
for pop in ['E', 'I']:
N = self.p['neuron']['N_'+pop]
dtheta = deg2rad(angle_diff(stimparams['theta_stim'], np.arange(N)/N*360., 'deg'))
self.Istim[pop] = (stimparams['I0_'+pop] +
stimparams['I1_'+pop] * np.exp(stimparams['mu']*(np.cos(dtheta)-1)))
#/////////////////////////////////////////////////////////////////////////////////////////
if __name__ == '__main__':
dt = 0.2*ms
T = 1.5*second
# Setup the network
model = Model(modelparams, stimparams, dt)
network = Network(model)
# Setup the stimulus parameters for this trial (optional)
model.stimparams['theta_stim'] = 180
#model.stimparams['sigma_stim'] = 14
#model.stimparams['Ipeak'] = 500*pA
model.reinit(seed=1234)
network.run(T, report='text')
# Plot results
plt.figure()
spike_id, spike_time = zip(*model.mons['spikeE'].spikes)
plt.plot(spike_time, spike_id, 'o', ms=2, mfc='k', mew=0)
plt.ylim([min(spike_id),max(spike_id)])
plt.xlabel('Time (second)')
plt.ylabel('Neuron index')
#plt.savefig('workingmemory_ringmodel.pdf')
#==============================================================================
# p = model.p
# w = dict()
# for area in areas:
# JEE_plus = p[area]['JEE_plus'] # PFC and MT the same
# sigma_EE = deg2rad(p[area]['sigma_EE'])
#
# tmp = (2*scipy.stats.norm.cdf(np.pi/sigma_EE)-1)/np.sqrt(2*np.pi)*sigma_EE
# JEE_minus = (1-JEE_plus*tmp)/(1-tmp)
#
# dtheta = 2*np.pi*((np.arange(N_E)+1)/N_E-0.5)
# w[area] = JEE_minus+((JEE_plus-JEE_minus)*np.exp(-dtheta**2/2./sigma_EE**2))
#==============================================================================
N0 = 16
N1 = 4
d0 = 2*np.pi*((np.arange(N0)+1)/N0-0.5)
d1 = 2*np.pi*((np.arange(N1)+1)/N1-0.5)
|
xjwanglab/book
|
ardid2007/ardid2007.py
|
Python
|
mit
| 16,728
|
[
"Brian",
"NEURON"
] |
3b7f896a0630efa12156bb4e1326d043f6b59546fea6c682a0fdbb93e48f07b0
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# ePuck.py
#
# Copyright 2010 Manuel Martín Ortiz <manuel.martin@itrblabs.eu>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
# -- ePuck.py --
#
# The aim of this library is to provide access to the ePuck robots
# through a bluetooth connection. Thus, you can write a program that
# read from the ePuck's sensors and write in their actuators, This
# will allow us to create advanced programs that can develop a wide
# variety of complex tasks. It is necesary that the ePuck has installed
# the Webot's fimware 1.4.2 or 1.4.3. You can find this fantastic
# simulator on this site: http://www.cyberbotics.com/
#
# This library is written in Python 2.6, and you can import it from
# any program written in Python (same version or later). In addition
# to this, you will also need two extra libraries:
#
# -> Python Bluetooth or Pybluez
# -> Python Image Library (PIL)
#
# In this package you will find some examples of how to use this library.
#
# You may experience some problems when you work with your ePuck, We
# recommend you take into consideration the following special
# characteristic: we use a bluetooth communciation, therefore our bandwith
# is limited and we cannot expect to do too many tasks in short
# time; i.e: If you put the wheels speed to max and want
# to make a quick process of the images, you will know what I'm saying.
# So remember, you are processing in your computer, not on the ePuck,
# and you need to take the sensors data and write on the actuators
# values on the ePuck
#
# For further information and updates visit http://www.itrblabs.eu
import sys # System library
import serial # Used for communications
import time # Used for image capture process
import struct # Used for Big-Endian messages
import Image # Used for the pictures of the camera
import i2c # Ground sensors are directly connected to the overo's i2c bus
__package__ = "ePuck"
__docformat__ = "restructuredtext"
"""
:newfield company: Company
"""
__version__ = "1.2.2+gumstix-sercom-1"
__author__ = "Manuel Martin Ortiz"
__license__ = "GPL"
__company__ = "RTDI - ITRB Labs"
__contact__ = ["manuel.martin@itrblabs.eu"]
# This dictionary have as keys the first character of the message, that
# is used to know the number of lines. If no key for the message, 1 line is assumed
DIC_MSG = {
"v": 2, # Version
"\n": 23, # Menu
"\x0c": 2, # Welcome
"k": 3, # Calibration
"R": 2 # Reset
}
# You have to use the keys of this dictionary for indicate on "enable" function
# the sensor that you want to read
DIC_SENSORS = {
"accelerometer" : "a",
"selector" : "c",
"motor_speed" : "e",
"camera" : "i",
"floor" : "m",
"proximity" : "n",
"light" : "o",
"motor_position" : "q",
"microphone" : "u"
}
# You have to use the keys of this dictionary for indicate the operating
# mode of the camera
CAM_MODE = {
"GREY_SCALE" : 0,
"RGB_365" : 1,
"YUV" : 2,
"LINEAR_CAM" : 3
}
# You can use three different Zooms in the camera
CAM_ZOOM = (1, 4, 8)
class ePuck():
"""
This class represent an ePuck object
"""
def __init__(self, ttydev="/dev/ttyS0", debug=False):
"""
Constructor process
:param ttydev: Serial device to control robot, e.g. /dev/ttyS0
:type address: String
:param debug: If you want more verbose information, useful for debugging
:type debug: Boolean
:return: ePuck object
"""
# Monitoring Variables
self.messages_sent = 0
self.messages_received = 0
self.version = __version__
self.debug = debug
# Connection Attributes
self.ttydev = ttydev
self.conexion_status = False
# Camera attributes
self._cam_width = None
self._cam_height = None
self._cam_enable = False
self._cam_zoom = None
self._cam_mode = None
self._cam_size = None
# Sensors and actuators lists
self._sensors_to_read = []
self._actuators_to_write = []
# Floor sensor i2c bus & device
self._i2cbus = None
self._i2cdev = None
# Sensors
self._accelerometer = (0, 0, 0)
self._accelerometer_filtered = False
self._selector = (0)
self._motor_speed = (0, 0) # left and right motor
self._motor_position = (0, 0) # left and right motor
self._camera_parameters = (0, 0, 0, 0)
self._floor_sensors = (0, 0, 0)
self._proximity = (0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
self._light_sensor = (0, 0, 0, 0, 0, 0, 0, 0)
self._microphone = (0, 0, 0)
self._pil_image = None
# Leds
self._leds_status = [False] * 10
#
# Private methods
#
def _debug(self, *txt):
"""
Show debug information and data, only works if debug information
is enable (see "set_debug()")
:param txt: Data to be showed separated by comma
:type txt: Any
"""
if self.debug:
print >> sys.stderr, '\033[31m[ePuck]:\033[0m ', ' '.join([str(e) for e in txt])
return 0
def _recv(self, n=4096):
"""
Receive data from the robot
:param n: Number of bytes you want to receive
:type n: int
:return: Data received from the robot as string if it was successful, raise an exception if not
:rtype: String
:raise Exception: If there is a communication problem
"""
if not self.conexion_status:
raise Exception, 'There is not connection'
try:
line = self.serport.read(n)
self.messages_received += 1
except serial.SerialException as e:
txt = 'Serial communication problem: ' + str(e)
self._debug(txt)
raise Exception, txt
else:
return line
def _send(self, message):
"""
Send data to the robot
:param message: Message to be sent
:type message: String
:return: Number of bytes sent if it was successful. -1 if not
:rtype: int
"""
if not self.conexion_status:
raise Exception, 'There is not connection'
try:
n = self.serport.write(message)
self.messages_sent += 1
except Exception, e:
self._debug('Send problem:', e)
return -1
else:
return n
def _read_image(self):
"""
Returns an image obtained from the robot's camera. For communication
issues you only can get 1 image per second
:return: The image in PIL format
:rtype: PIL Image
"""
# Thanks to http://www.dailyenigma.org/e-puck-cam.shtml for
# the code for get the image from the camera
msg = struct.pack(">bb", -ord("I"), 0)
try:
n = self._send(msg)
self._debug("Reading Image: sending " + repr(msg) + " and " + str(n) + " bytes")
# We have to add 3 to the size, because with the image we
# get "mode", "width" and "height"
size = self._cam_size + 3
img = self._recv(size)
while len(img) != size:
img += self._recv(size)
# Create the PIL Image
image = Image.frombuffer("RGB", (self._cam_width, self._cam_height),
img, "raw",
"BGR;16", 0, 1)
image = image.rotate(180)
self._pil_image = image
except Exception, e:
self._debug('Problem receiving an image: ', e)
def _refresh_camera_parameters(self):
"""
Method for refresh the camera parameters, it's called for some
private methods
"""
try:
msg = self.send_and_receive("I").split(',')
except:
return False
else:
self._cam_mode, \
self._cam_width, \
self._cam_height, \
self._cam_zoom, \
self._cam_size = [int(i) for i in msg[1:6]]
self._camera_parameters = self._cam_mode, self._cam_width, self._cam_height, self._cam_zoom
def _write_actuators(self):
"""
Write in the robot the actuators values. Don't use directly,
instead use 'step()'
"""
# Not all messages reply with ACK, only Ascii messages
acks = ['j', 't']
# We make a copy of the actuators list
actuators = self._actuators_to_write[:]
for m in actuators:
if m[0] == 'L':
# Leds
msg = struct.pack('<bbb', -ord(m[0]), m[1], m[2])
n = self._send(msg)
self._debug('Binary message sent of [' + str(n) + '] bytes: ' + str(struct.unpack('<bbb', msg)))
elif m[0] == 'D' or m[0] == 'P':
# Set motor speed or set motor position
msg = struct.pack('<bhh', -ord(m[0]), m[1], m[2])
n = self._send(msg)
self._debug('Binary message sent of [' + str(n) + '] bytes: ' + str(struct.unpack('<bhh', msg)))
else:
# Others actuators, parameters are separated by commas
msg = ",".join(["%s" % i for i in m])
reply = self.send_and_receive(msg)
if reply == 'j':
self._refresh_camera_parameters()
if reply not in acks:
self._debug('Unknown ACK reply from ePcuk: ' + reply)
self._actuators_to_write.remove(m)
return
def _read_sensors(self):
"""
This method is used for read the ePuck's sensors. Don't use directly,
instead use 'step()'
"""
# We can read sensors in two ways: Binary Mode and Ascii Mode
# Ascii mode is slower than Binary mode, therefore, we use
# Binary mode whenever we can. Not all sensors are available in
# Binary mode
def send_binary_mode(parameters):
# Auxiliar function for sent messages in binary modes
# Parameters: ('Char to be sent', 'Size of reply waited', 'Format of the teply')
self._debug('Sending binary message: ', ','.join('%s' % i for i in parameters))
message = struct.pack(">bb", -ord(parameters[0]), 0)
self._send(message)
reply = self._recv()
while len(reply) < parameters[1]:
reply += self._recv()
reply = struct.unpack(parameters[2], reply)
self._debug('Binary message received: ', reply)
return reply
# Read different sensors
for s in self._sensors_to_read:
if s == 'a':
# Accelerometer sensor in a non filtered way
if self._accelerometer_filtered:
parameters = ('A', 12, '@III')
else:
parameters = ('a', 6, '@HHH')
reply = send_binary_mode(parameters)
if type(reply) is tuple and type(reply[0]) is int:
self._accelerometer = reply
elif s == 'n':
# Proximity sensors
parameters = ('N', 20, '@HHHHHHHHHH')
reply = send_binary_mode(parameters)
if type(reply) is tuple and type(reply[0]) is int:
self._proximity = reply
elif s == 'm':
# Floor sensors
#parameters = ('M', 6, '@HHH')
#reply = send_binary_mode(parameters)
#if type(reply) is tuple and type(reply[0]) is int:
# self._floor_sensors = reply
floor1 = (self._i2cdev[0] << 8) + self._i2cdev[1]
floor2 = (self._i2cdev[2] << 8) + self._i2cdev[3]
floor3 = (self._i2cdev[4] << 8) + self._i2cdev[5]
self._floor_sensors = (floor1, floor2, floor3)
elif s == 'q':
# Motor position sensor
parameters = ('Q', 4, '@HH')
reply = send_binary_mode(parameters)
if type(reply) is tuple and type(reply[0]) is int:
self._motor_position = reply
elif s == 'o':
# Light sensors
parameters = ('O', 16, '@HHHHHHHH')
reply = send_binary_mode(parameters)
if type(reply) is tuple and type(reply[0]) is int:
self._light_sensor = reply
elif s == 'u':
# Microphone
parameters = ('u', 6, '@HHH')
reply = send_binary_mode(parameters)
if type(reply) is tuple and type(reply[0]) is int:
self._microphone = reply
elif s == 'e':
# Motor Speed
parameters = ('E', 4, '@HH')
reply = send_binary_mode(parameters)
if type(reply) is tuple and type(reply[0]) is int:
self._motor_speed = reply
elif s == 'i':
# Do nothing for the camera, is an independent process
pass
else:
reply = self.send_and_receive(s).split(",")
t = reply[0]
response = tuple(reply[1:len(reply)])
if t == "c":
# Selector
self._selector = response[0]
else:
self._debug('Unknow type of sensor to read' + str(reply))
#
# Public methods
#
def connect(self):
"""
Connect with the physic ePuck robot
:return: If the connexion was succesful
:rtype: Boolean
:except Exception: If there are a communication problem, for example, the robot is off
"""
if self.conexion_status:
self._debug('Already connected')
return False
try:
self.serport = serial.Serial(0)#serial.serial_for_url(self.ttydev)
self.serport.baudrate = 230400
self.serport.timeout = 0.5
except Exception, e:
txt = 'Connection problem: \n' + str(e)
self._debug(txt)
raise Exception, txt
self.conexion_status = True
self._debug("Connected")
self.reset()
return True
def disconnect(self):
"""
Disconnect from ePuck robot. Same as 'close()'
"""
self.close()
def close(self):
"""
Close the connection with the robot. Same as 'disconnect()'
:return: 0 if all ok
:rtype: int
:raise Exception: if it was a problem closing the connection
"""
if self.conexion_status:
try:
# Stop the robot
self._debug("Timeout: " + str(self.serport.timeout))
self.stop()
# Close the socket
self.serport.close()
self.conexion_status = False
except Exception, e:
raise Exception, 'Closing connection problem: \n' + str(e)
else:
return 0
def set_debug(self, debug):
"""
Set / unset debug information
:param debug: True or False, as you want or not Debug information
:type debug: Boolean
"""
self.debug = debug
def send_and_receive(self, msg):
"""
Send an Ascii message to the robot and return the reply. You can
use it, but I don't recommend, use 'enable()', 'disable()'
and 'step()' instead
:param msg: The message you want to send
:type msg: String
:return: Response of the robot
:rtype: String
"""
# Check the connection
if not self.conexion_status:
raise Exception, 'There is not connection'
# Make sure the Message is a string
message = str(msg)
# Add carriage return if not
if not message.endswith('\n'):
message += '\n'
# Check the lines of the waited reply
if message[0] in DIC_MSG:
lines = DIC_MSG[message[0]]
else:
lines = 1
self._debug('Waited lines:', lines)
# We make 5 tries before desist
tries = 1
while tries < 5:
# Send the message
bytes = self._send(message)
self._debug('Message sent:', repr(message))
self._debug('Bytes sent:', bytes)
try:
# Receive the reply. As we want to receive a line, we have to insist
reply = ''
while reply.count('\n') < lines:
reply += self._recv()
if message[0] == 'R':
# For some reason that I don't understand, if you send a reset
# command 'R', sometimes you recive 1 or 2 lines of 'z,Command not found\r\n'
# Therefore I have to remove it from the expected message: The Hello message
reply = reply.replace('z,Command not found\r\n', '')
self._debug('Message received: ', reply)
return reply.replace('\r\n', '')
except Exception, e:
tries += 1
self._debug('Communication timeout, retrying')
def save_image(self, name='ePuck.jpg'):
"""
Save image from ePuck's camera to disk
:param name: Image name, ePuck.jpg as default
:type name: String
:return: Operation result
:rtype: Boolean
"""
if self._pil_image:
return self._pil_image.save(name)
else:
return False
def get_accelerometer(self):
"""
Return Accelerometer values in (x, y, z)
:return: Accelerometer values
:rtype: Tuple
"""
return self._accelerometer
def get_selector(self):
"""
Return the selector position (0-15)
:return: Selector value
:rtype: int
"""
return self._selector
def get_motor_speed(self):
"""
Return the motor speed. Correct values are in the range [-1000, 1000]
:return: Motor speed
:rtype: Tuple
"""
return self._motor_speed
def get_camera_parameters(self):
"""
Return the camera parameters as a tuple
(mode, width, height, zoom)
:return: Camera parameters
:rtype: Tuple
"""
return self._camera_parameters
def get_floor_sensors(self):
"""
Return the floor sensors values as (left, center, right)
:return: Floor sensors values
:rtype: Tuple
"""
return self._floor_sensors
def get_proximity(self):
"""
Return the values of the 8 proximity sensors
:return: Proximity sensors values
:rtype: Tuple
"""
return self._proximity
def get_light_sensor(self):
"""
Return the value of the light sensor
:return: Ligth sensor value
:rtype: Tuple
"""
return self._light_sensor
def get_motor_position(self):
"""
Return the position of the left and right motor as a tuple
:return: Motor position
:rtype: Tuple
"""
return self._motor_position
def get_microphone(self):
"""
Return the volume of the three microphones
:return: Microphones values
:rtype: Tuple
"""
return self._microphone
def is_connected(self):
"""
Return a boolean value that indicate if the robot is connected to the PC
:return: If the robot is connected to the PC
:rtype: Boolean
"""
return self.conexion_status
def get_image(self):
"""
Return the last image captured from the ePuck's camera (after a 'step()').
None if there are not images captured. The image is an PIL object
:return: Image from robot's camera
:rtype: PIL
"""
return self._pil_image
def get_sercom_version(self):
"""
:return: Return the ePuck's firmware version
:rtype: String
"""
return self.send_and_receive("v")
def set_accelerometer_filtered(self, filter=False):
"""
Set filtered way for accelerometer, False is default value
at the robot start
:param filter: True or False, as you want
:type filter: Boolean
"""
self._accelerometer_filtered = filter
def disable(self, *sensors):
"""
Sensor(s) that you want to get disable in the ePuck
:param sensors: Name of the sensors, take a look to DIC_SENSORS. Multiple sensors can be separated by commas
:type sensors: String
:return: Sensors enabled
:rtype: List
:except Exception: Some wrong happened
"""
for sensor in sensors:
try:
if not DIC_SENSORS.has_key(sensor):
self._debug('Sensor "' + sensor + '" not in DIC_SENSORS')
break
if sensor == "camera":
self._cam_enable = False
if DIC_SENSORS[sensor] in self._sensors_to_read:
l = list(self._sensors_to_read)
l.remove(DIC_SENSORS[sensor])
self._sensors_to_read = tuple(l)
self._debug('Sensor "' + sensor + '" disabled')
else:
self._debug('Sensor "' + sensor + '" alrady disabled')
except Exception, e:
self._debug('Something wrong happened to disable the sensors: ', e)
return self.get_sensors_enabled()
def enable(self, *sensors):
"""
Sensor(s) that you want to get enable in the ePuck
:param sensors: Name of the sensors, take a look to DIC_SENSORS. Multiple sensors can be separated by commas
:type sensors: String
:return: Sensors enabled
:rtype: List
:except Exception: Some wrong happened
"""
# Using the * as a parameters, we get a tuple with all sensors
for sensor in sensors:
try:
if not DIC_SENSORS.has_key(sensor):
self._debug('Sensor "' + sensor + '" not in DIC_SENSORS')
break
if sensor == "camera":
# If the sensor is the Camera, then we refresh the
# camera parameters
if not self._cam_enable:
try:
self._refresh_camera_parameters()
self._cam_enable = True
self.timestamp = time.time()
except:
break
if sensor == "floor" and self._i2cbus == None:
# Initialize i2c bus
self._i2cbus = i2c.I2cBus(3)
self._i2cdev = self._i2cbus[0x60]
if DIC_SENSORS[sensor] not in self._sensors_to_read:
l = list(self._sensors_to_read)
l.append(DIC_SENSORS[sensor])
self._sensors_to_read = tuple(l)
self._debug('Sensor "' + sensor + '" enabled')
else:
self._debug('Sensor "' + sensor + '" alrady enabled')
except Exception, e:
self._debug('Something wrong happened to enable the sensors: ', e)
return self.get_sensors_enabled()
def get_sensors_enabled(self):
"""
:return: Return a list of sensors thar are active
:rtype: List
"""
l = []
for sensor in DIC_SENSORS:
if DIC_SENSORS[sensor] in self._sensors_to_read:
l.append(sensor)
return l
def set_motors_speed(self, l_motor, r_motor):
"""
Set the motors speed. The MAX and MIN speed of the ePcuk is [-1000, 1000]
:param l_motor: Speed of left motor
:type l_motor: int
:param r_motor: Speed of right motor
:type r_motor: int
"""
# I don't check the MAX and MIN speed because this check
# will be made by the ePuck's firmware. Here we need speed
# and we lose time mading recurrent chekings
self._actuators_to_write.append(("D", int(l_motor), int(r_motor)))
return True
def set_motor_position(self, l_wheel, r_wheel):
"""
Set the motor position, useful for odometry
:param l_wheel: left wheel
:type l_wheel: int
:param r_wheel: right wheel
:type r_wheel: int
"""
self._actuators_to_write.append(("P", l_wheel, r_wheel))
def set_led(self, led_number, led_value):
"""
Turn on/off the leds
:param led_number: If led_number is other than 0-7, all leds are set to the indicated value.
:type led_number: int
:param led_value:
- 0 : Off
- 1 : On (Red)
- 2 : Inverse, does not work for all leds
:type led_value: int
"""
led = abs(led_number)
value = abs(led_value)
if led < 11:
if led <= 7:
self._actuators_to_write.append(("L", led, value))
else:
self._actuators_to_write.append(("L", 10, value))
for i in range(8):
if value == 0:
self._leds_status[i] = False
elif value == 1:
self._leds_status[i] = True
if value == 0:
self._leds_status[led] = False
elif value == 1:
self._leds_status[led] = True
else:
self._leds_status[led] = not self._leds_status[led]
return True
else:
return False
def set_body_led(self, led_value):
"""
Turn on /off the body led
:param led_value:
- 0 : Off
- 1 : On (green)
- 2 : Inverse
:type led_value: int
"""
value = abs(led_value)
self._actuators_to_write.append(("L", 8, value))
if value == 0:
self._leds_status[8] = False
elif value == 1:
self._leds_status[8] = True
else:
self._leds_status[8] = not self._leds_status[8]
return True
def set_front_led(self, led_value):
"""
Turn on /off the front led
:type led_value: int
:param led_value:
- 0 : Off
- 1 : On (green)
- 2 : Inverse
"""
value = abs(led_value)
self._actuators_to_write.append(("L", 9, value))
if value == 0:
self._leds_status[9] = False
elif value == 1:
self._leds_status[9] = True
else:
self._leds_status[9] = not self._leds_status[9]
return True
def set_sound(self, sound):
"""
Reproduce a sound
:param sound: Sound in the range [1,5]. Other for stop
:type sound: int
"""
self._actuators_to_write.append(("T", sound))
return True
def set_camera_parameters(self, mode, width, height, zoom):
"""
Set the camera parameters
:param mode: GREY_SCALE, LINEAR_CAM, RGB_365, YUM
:type mode: String
:param width: Width of the camera
:type width: int
:param height: Height of the camera
:type height: int
:param zoom: 1, 4, 8
:type zoom: int
"""
if mode in CAM_MODE:
self._cam_mode = CAM_MODE[mode]
else:
self._debug(ERR_CAM_PARAMETERS, "Camera mode")
return -1
if int(zoom) in CAM_ZOOM:
self._cam_zoom = zoom
else:
self._debug(ERR_CAM_PARAMETERS, "Camera zoom")
return -1
if self.conexion_status and int(width) * int(height) <= 1600:
# 1600 are for the resolution no greater than 40x40, I have
# detect some problems
self._actuators_to_write.append(("J",
self._cam_mode,
width,
height,
self._cam_zoom))
return 0
def calibrate_proximity_sensors(self):
"""
Calibrate proximity sensors, keep off any object in 10 cm
:return: Successful operation
:rtype: Boolean
"""
reply = self.send_and_receive("k", tries_timeout=25)
if reply[1] == "k":
return True
else:
return False
def reset(self):
"""
Reset the robot
:return: Successful operation
:rtype: Boolean
:raise Exception: If there is not connection
"""
if not self.conexion_status:
raise Exception, 'There is not connection'
msg = self.send_and_receive("R")
self._debug(msg)
return True
def stop(self):
"""
Stop the motor and turn off all leds
:return: Successful operation
:rtype: Boolean
:raise Exception: If there is not connection
"""
if not self.conexion_status:
raise Exception, 'There is not connection'
reply = self.send_and_receive("S")
self._debug(reply)
if reply == "s":
return True
else:
return False
def step(self):
"""
Method to update the sensor readings and to reflect changes in
the actuators. Before invoking this method is not guaranteed
the consistency of the sensors
"""
if not self.conexion_status:
raise Exception, 'There is not connection'
self._write_actuators()
self._read_sensors()
# Get an image in 1 FPS
if self._cam_enable and time.time() - self.timestamp > 1:
self._read_image()
self.timestamp = time.time()
|
FlorianNaumann/ePuck_Sercom_cpp
|
ePuck.py
|
Python
|
gpl-3.0
| 25,529
|
[
"VisIt"
] |
42eec46babb73f549fe2af378a36b6efc8f35f335eb47da2467e456b018a08af
|
__author__ = 'Robert Meyer'
from brian import *
def run_network():
clear(True, True)
monitor_dict={}
defaultclock.dt= 0.01*ms
C=281*pF
gL=30*nS
EL=-70.6*mV
VT=-50.4*mV
DeltaT=2*mV
tauw=40*ms
a=4*nS
b=0.08*nA
I=8*nA
Vcut=DeltaT# practical threshold condition
N=10
reset = 'vm=Vr;w+=b'
eqs="""
dvm/dt=(gL*(EL-vm)+gL*DeltaT*exp((vm-VT)/DeltaT)+I-w)/C : volt
dw/dt=(a*(vm-EL)-w)/tauw : amp
Vr:volt
"""
neuron=NeuronGroup(N,model=eqs,threshold=Vcut,reset=reset)
neuron.vm=EL
neuron.w=a*(neuron.vm-EL)
neuron.Vr=linspace(-48.3*mV,-47.7*mV,N) # bifurcation parameter
#run(25*msecond,report='text') # we discard the first spikes
MSpike=SpikeMonitor(neuron, delay = 1*ms) # record Vr and w at spike times
MPopSpike =PopulationSpikeCounter(neuron, delay = 1*ms)
MPopRate = PopulationRateMonitor(neuron,bin=5*ms)
MStateV = StateMonitor(neuron,'vm',record=[1,2,3])
MStatewMean = StateMonitor(neuron,'w',record=False)
MRecentStateV = RecentStateMonitor(neuron,'vm',record=[1,2,3],duration=10*ms)
MRecentStatewMean = RecentStateMonitor(neuron,'w',duration=10*ms,record=False)
MCounts = SpikeCounter(neuron)
MStateSpike = StateSpikeMonitor(neuron,('w','vm'))
MMultiState = MultiStateMonitor(neuron,['w','vm'],record=[6,7,8,9])
ISIHist = ISIHistogramMonitor(neuron,[0,0.0001,0.0002], delay = 1*ms)
VanRossum = VanRossumMetric(neuron, tau=5*msecond)
run(10*msecond,report='text')
monitor_dict['SpikeMonitor']=MSpike
monitor_dict['SpikeMonitorAr']=MSpike
monitor_dict['PopulationSpikeCounter']=MPopSpike
monitor_dict['PopulationRateMonitor']=MPopRate
monitor_dict['StateMonitorV']=MStateV
monitor_dict['StateMonitorwMean']=MStatewMean
monitor_dict['Counts']=MCounts
monitor_dict['StateSpikevmw']=MStateSpike
monitor_dict['StateSpikevmwAr']=MStateSpike
monitor_dict['MultiState']=MMultiState
monitor_dict['ISIHistogrammMonitor']=ISIHist
monitor_dict['RecentStateMonitorV']=MRecentStateV
monitor_dict['RecentStateMonitorwMean']=MRecentStatewMean
monitor_dict['VanRossumMetric']=VanRossum
return monitor_dict
|
nigroup/pypet
|
pypet/tests/unittests/briantests/run_a_brian_network.py
|
Python
|
bsd-3-clause
| 2,219
|
[
"Brian",
"NEURON"
] |
25862f9f60803512f525046197082bc2f611014daf690ee7c50968eec3fed86f
|
#!/usr/local/bin/python
#CHIPSEC: Platform Security Assessment Framework
#Copyright (c) 2010-2015, Intel Corporation
#
#This program is free software; you can redistribute it and/or
#modify it under the terms of the GNU General Public License
#as published by the Free Software Foundation; Version 2.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with this program; if not, write to the Free Software
#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
#Contact information:
#chipsec@intel.com
#
"""
.. note:: THIS FILE WAS GENERATED
Auto generated from:
http://www.pcidatabase.com/vendors.php?sort=id
http://www.pcidatabase.com/reports.php?type=csv
"""
VENDORS = {
0x0033 : "Paradyne Corp.",
0x003D : "master",
0x0070 : "Hauppauge Computer Works Inc.",
0x0100 : "USBPDO-8",
0x0123 : "General Dynamics",
0x0315 : "SK - Electronics Co., Ltd.",
0x0402 : " Acer aspire one",
0x046D : "Logitech Inc.",
0x0483 : "UPEK",
0x04A9 : "Canon",
0x04B3 : "IBM",
0x04D9 : "Filco",
0x04F2 : "Chicony Electronics Co. ",
0x051D : "APC",
0x0529 : "Aladdin E-Token",
0x0553 : " Aiptek USA",
0x058f : "Alcor Micro Corp.",
0x0590 : "Omron Corp",
0x05ac : "Apple, Inc.",
0x05E1 : "D-MAX",
0x064e : "SUYIN Corporation",
0x067B : "Prolific Technology Inc.",
0x06FE : "Acresso Software Inc.",
0x0711 : "SIIG, Inc.",
0x093a : "KYE Systems Corp.",
0x096E : "USB Rockey dongle from Feitain ",
0x0A5C : "Broadcom Corporation",
0x0A89 : "BREA Technologies Inc.",
0x0A92 : "Egosys, Inc.",
0x0AC8 : "ASUS ",
0x0b05 : "Toshiba Bluetooth RFBUS, RFCOM, RFHID",
0x0c45 : "Microdia Ltd.",
0x0cf3 : "TP-Link",
0x0D2E : "Feedback Instruments Ltd.",
0x0D8C : "C-Media Electronics, Inc.",
0x0DF6 : "Sitecom",
0x0E11 : "dell Computer Corp.",
0x0E8D : "MediaTek Inc.",
0x1000 : "LSI Logic",
0x1001 : "Kolter Electronic - Germany",
0x1002 : "Advanced Micro Devices, Inc.",
0x1003 : "ULSI",
0x1004 : "VLSI Technology",
0x1006 : "Reply Group",
0x1007 : "Netframe Systems Inc.",
0x1008 : "Epson",
0x100A : "as Ltd. de Phoenix del de Tecnolog",
0x100B : "National Semiconductors",
0x100C : "Tseng Labs",
0x100D : "AST Research",
0x100E : "Weitek",
0x1010 : "Video Logic Ltd.",
0x1011 : "Digital Equipment Corporation",
0x1012 : "Micronics Computers Inc.",
0x1013 : "Cirrus Logic",
0x1014 : "International Business Machines Corp.",
0x1016 : "Fujitsu ICL Computers",
0x1017 : "Spea Software AG",
0x1018 : "Unisys Systems",
0x1019 : "Elitegroup Computer System",
0x101A : "NCR Corporation",
0x101B : "Vitesse Semiconductor",
0x101E : "American Megatrends Inc.",
0x101F : "PictureTel Corp.",
0x1020 : "Hitachi Computer Electronics",
0x1021 : "Oki Electric Industry",
0x1022 : "Advanced Micro Devices",
0x1023 : "TRIDENT MICRO",
0x1025 : "Acer Incorporated",
0x1028 : "Toshiba Satellite A660",
0x102A : "LSI Logic Headland Division",
0x102B : "Matrox Electronic Systems Ltd.",
0x102C : "Asiliant (Chips And Technologies)",
0x102D : "Wyse Technologies",
0x102E : "Olivetti Advanced Technology",
0x102F : "Toshiba America",
0x1030 : "TMC Research",
0x1031 : "miro Computer Products AG",
0x1033 : "NEC Electronics",
0x1034 : "Burndy Corporation",
0x1036 : "Future Domain",
0x1037 : "Hitachi Micro Systems Inc",
0x1038 : "AMP Incorporated",
0x1039 : "SİS",
0x103A : "Seiko Epson Corporation",
0x103B : "Tatung Corp. Of America",
0x103C : "Hewlett-Packard - HP dc7800",
0x103E : "Solliday Engineering",
0x103F : "Logic Modeling",
0x1041 : "Computrend",
0x1043 : "Asustek Computer Inc.",
0x1044 : "Distributed Processing Tech",
0x1045 : "OPTi Inc.",
0x1046 : "IPC Corporation LTD",
0x1047 : "Genoa Systems Corp.",
0x1048 : "ELSA GmbH",
0x1049 : "Fountain Technology",
0x104A : "STMicroelectronics",
0x104B : "Mylex / Buslogic",
0x104C : "Texas Instruments",
0x104D : "Sony Corporation",
0x104E : "Oak Technology",
0x104F : "Co-Time Computer Ltd.",
0x1050 : "Winbond Electronics Corp.",
0x1051 : "Anigma Corp.",
0x1053 : "Young Micro Systems",
0x1054 : "Hitachi Ltd",
0x1055 : "Standard Microsystems Corp.",
0x1056 : "ICL",
0x1057 : "Motorola",
0x1058 : "Electronics & Telecommunication Res",
0x1059 : "Kontron Canada",
0x105A : "Promise Technology",
0x105B : "Foxconn International Inc.",
0x105C : "Wipro Infotech Limited",
0x105D : "Number Nine Visual Technology",
0x105E : "Vtech Engineering Canada Ltd.",
0x105F : "Infotronic America Inc.",
0x1060 : "United Microelectronics",
0x1061 : "8x8 Inc.",
0x1062 : "Maspar Computer Corp.",
0x1063 : "Ocean Office Automation",
0x1064 : "Alcatel Cit",
0x1065 : "Texas Microsystems",
0x1066 : "Picopower Technology",
0x1067 : "Mitsubishi Electronics",
0x1068 : "Diversified Technology",
0x106A : "Aten Research Inc.",
0x106B : "Apple Inc.",
0x106C : "Hyundai Electronics America",
0x106D : "Sequent Computer Systems",
0x106E : "DFI Inc.",
0x106F : "City Gate Development LTD",
0x1070 : "Daewoo Telecom Ltd.",
0x1071 : "Mitac",
0x1072 : "GIT Co. Ltd.",
0x1073 : "Yamaha Corporation",
0x1074 : "Nexgen Microsystems",
0x1075 : "Advanced Integration Research",
0x1077 : "QLogic Corporation",
0x1078 : "Cyrix Corporation",
0x1079 : "I-Bus",
0x107A : "Networth controls",
0x107B : "Gateway 2000",
0x107C : "Goldstar Co. Ltd.",
0x107D : "Leadtek Research",
0x107E : "Testernec",
0x107F : "Data Technology Corporation",
0x1080 : "Cypress Semiconductor",
0x1081 : "Radius Inc.",
0x1082 : "EFA Corporation Of America",
0x1083 : "Forex Computer Corporation",
0x1084 : "Parador",
0x1085 : "Tulip Computers Int'l BV",
0x1086 : "J. Bond Computer Systems",
0x1087 : "Cache Computer",
0x1088 : "Microcomputer Systems (M) Son",
0x1089 : "Data General Corporation",
0x108A : "SBS Operations",
0x108C : "Oakleigh Systems Inc.",
0x108D : "Olicom",
0x108E : "Sun Microsystems",
0x108F : "Systemsoft Corporation",
0x1090 : "Encore Computer Corporation",
0x1091 : "Intergraph Corporation",
0x1092 : "Diamond Computer Systems",
0x1093 : "National Instruments",
0x1094 : "Apostolos",
0x1095 : "Silicon Image, Inc.",
0x1096 : "Alacron",
0x1097 : "Appian Graphics",
0x1098 : "Quantum Designs Ltd.",
0x1099 : "Samsung Electronics Co. Ltd.",
0x109A : "Packard Bell",
0x109B : "Gemlight Computer Ltd.",
0x109C : "Megachips Corporation",
0x109D : "Zida Technologies Ltd.",
0x109E : "Brooktree Corporation",
0x109F : "Trigem Computer Inc.",
0x10A0 : "Meidensha Corporation",
0x10A1 : "Juko Electronics Inc. Ltd.",
0x10A2 : "Quantum Corporation",
0x10A3 : "Everex Systems Inc.",
0x10A4 : "Globe Manufacturing Sales",
0x10A5 : "Racal Interlan",
0x10A8 : "Sierra Semiconductor",
0x10A9 : "Silicon Graphics",
0x10AB : "Digicom",
0x10AC : "Honeywell IASD",
0x10AD : "Winbond Systems Labs",
0x10AE : "Cornerstone Technology",
0x10AF : "Micro Computer Systems Inc.",
0x10B0 : "Gainward GmbH ",
0x10B1 : "Cabletron Systems Inc.",
0x10B2 : "Raytheon Company",
0x10B3 : "Databook Inc.",
0x10B4 : "STB Systems",
0x10B5 : "PLX Technology Inc.",
0x10B6 : "Madge Networks",
0x10B7 : "3Com Corporation",
0x10B8 : "Standard Microsystems Corporation",
0x10B9 : "Ali Corporation",
0x10BA : "Mitsubishi Electronics Corp.",
0x10BB : "Dapha Electronics Corporation",
0x10BC : "Advanced Logic Research Inc.",
0x10BD : "Surecom Technology",
0x10BE : "Tsenglabs International Corp.",
0x10BF : "MOST Corp.",
0x10C0 : "Boca Research Inc.",
0x10C1 : "ICM Corp. Ltd.",
0x10C2 : "Auspex Systems Inc.",
0x10C3 : "Samsung Semiconductors",
0x10C4 : "Award Software Int'l Inc.",
0x10C5 : "Xerox Corporation",
0x10C6 : "Rambus Inc.",
0x10C8 : "Neomagic Corporation",
0x10C9 : "Dataexpert Corporation",
0x10CA : "Fujitsu Siemens",
0x10CB : "Omron Corporation",
0x10CD : "Advanced System Products",
0x10CF : "Fujitsu Ltd.",
0x10D1 : "Future+ Systems",
0x10D2 : "Molex Incorporated",
0x10D3 : "Jabil Circuit Inc.",
0x10D4 : "Hualon Microelectronics",
0x10D5 : "Autologic Inc.",
0x10D6 : "Wilson .co .ltd",
0x10D7 : "BCM Advanced Research",
0x10D8 : "Advanced Peripherals Labs",
0x10D9 : "Macronix International Co. Ltd.",
0x10DB : "Rohm Research",
0x10DC : "CERN-European Lab. for Particle Physics",
0x10DD : "Evans & Sutherland",
0x10DE : "vtrkavxfng",
0x10DF : "Emulex Corporation",
0x10E1 : "Tekram Technology Corp. Ltd.",
0x10E2 : "Aptix Corporation",
0x10E3 : "Tundra Semiconductor Corp.",
0x10E4 : "Tandem Computers",
0x10E5 : "Micro Industries Corporation",
0x10E6 : "Gainbery Computer Products Inc.",
0x10E7 : "Vadem",
0x10E8 : "Applied Micro Circuits Corp.",
0x10E9 : "Alps Electronic Corp. Ltd.",
0x10EA : "Tvia, Inc.",
0x10EB : "Artist Graphics",
0x10EC : "Realtek Semiconductor Corp.",
0x10ED : "Ascii Corporation",
0x10EE : "Xilinx Corporation",
0x10EF : "Racore Computer Products",
0x10F0 : "Curtiss-Wright Controls Embedded Computing",
0x10F1 : "Tyan Computer",
0x10F2 : "Achme Computer Inc. - GONE !!!!",
0x10F3 : "Alaris Inc.",
0x10F4 : "S-Mos Systems",
0x10F5 : "NKK Corporation",
0x10F6 : "Creative Electronic Systems SA",
0x10F7 : "Matsushita Electric Industrial Corp.",
0x10F8 : "Altos India Ltd.",
0x10F9 : "PC Direct",
0x10FA : "Truevision",
0x10FB : "Thesys Microelectronic's",
0x10FC : "I-O Data Device Inc.",
0x10FD : "Soyo Technology Corp. Ltd.",
0x10FE : "Fast Electronic GmbH",
0x10FF : "Ncube",
0x1100 : "Jazz Multimedia",
0x1101 : "Initio Corporation",
0x1102 : "Creative Technology LTD.",
0x1103 : " HighPoint Technologies, Inc.",
0x1104 : "Rasterops",
0x1105 : "Sigma Designs Inc.",
0x1106 : "VIA Technologies, Inc.",
0x1107 : "Stratus Computer",
0x1108 : "Proteon Inc.",
0x1109 : "Adaptec/Cogent Data Technologies",
0x110A : "Siemens Nixdorf AG",
0x110B : "Chromatic Research Inc",
0x110C : "Mini-Max Technology Inc.",
0x110D : "ZNYX Corporation",
0x110E : "CPU Technology",
0x110F : "Ross Technology",
0x1112 : "Osicom Technologies Inc.",
0x1113 : "Accton Technology Corporation",
0x1114 : "Atmel Corp.",
0x1116 : "Data Translation, Inc.",
0x1117 : "Datacube Inc.",
0x1118 : "Berg Electronics",
0x1119 : "ICP vortex Computersysteme GmbH",
0x111A : "Efficent Networks",
0x111C : "Tricord Systems Inc.",
0x111D : "Integrated Device Technology Inc.",
0x111F : "Precision Digital Images",
0x1120 : "EMC Corp.",
0x1121 : "Zilog",
0x1123 : "Excellent Design Inc.",
0x1124 : "Leutron Vision AG",
0x1125 : "Eurocore/Vigra",
0x1127 : "FORE Systems",
0x1129 : "Firmworks",
0x112A : "Hermes Electronics Co. Ltd.",
0x112C : "Zenith Data Systems",
0x112D : "Ravicad",
0x112E : "Infomedia",
0x1130 : "Computervision",
0x1131 : "NXP Semiconductors N.V.",
0x1132 : "Mitel Corp.",
0x1133 : "Eicon Networks Corporation",
0x1134 : "Mercury Computer Systems Inc.",
0x1135 : "Fuji Xerox Co Ltd",
0x1136 : "Momentum Data Systems",
0x1137 : "Cisco Systems Inc",
0x1138 : "Ziatech Corporation",
0x1139 : "Dynamic Pictures Inc",
0x113A : "FWB Inc",
0x113B : "Network Computing Devices",
0x113C : "Cyclone Microsystems Inc.",
0x113D : "Leading Edge Products Inc",
0x113E : "Sanyo Electric Co",
0x113F : "Equinox Systems",
0x1140 : "Intervoice Inc",
0x1141 : "Crest Microsystem Inc",
0x1142 : "Alliance Semiconductor",
0x1143 : "Netpower Inc",
0x1144 : "Cincinnati Milacron",
0x1145 : "Workbit Corp",
0x1146 : "Force Computers",
0x1147 : "Interface Corp",
0x1148 : "Marvell Semiconductor Germany GmbH",
0x1149 : "Win System Corporation",
0x114A : "VMIC",
0x114B : "Canopus corporation",
0x114C : "Annabooks",
0x114D : "IC Corporation",
0x114E : "Nikon Systems Inc",
0x114F : "Digi International",
0x1150 : "Thinking Machines Corporation",
0x1151 : "JAE Electronics Inc.",
0x1153 : "Land Win Electronic Corp",
0x1154 : "Melco Inc",
0x1155 : "Pine Technology Ltd",
0x1156 : "Periscope Engineering",
0x1157 : "Avsys Corporation",
0x1158 : "Voarx R&D Inc",
0x1159 : "Mutech",
0x115A : "Harlequin Ltd",
0x115B : "Parallax Graphics",
0x115C : "Photron Ltd.",
0x115D : "Xircom",
0x115E : "Peer Protocols Inc",
0x115F : "Maxtor Corporation",
0x1160 : "Megasoft Inc",
0x1161 : "PFU Ltd",
0x1162 : "OA Laboratory Co Ltd",
0x1163 : "mohamed alsherif",
0x1164 : "Advanced Peripherals Tech",
0x1165 : "Imagraph Corporation",
0x1166 : "Broadcom / ServerWorks",
0x1167 : "Mutoh Industries Inc",
0x1168 : "Thine Electronics Inc",
0x1169 : "Centre f/Dev. of Adv. Computing",
0x116A : "Luminex Software, Inc",
0x116B : "Connectware Inc",
0x116C : "Intelligent Resources",
0x116E : "Electronics for Imaging",
0x1170 : "Inventec Corporation",
0x1172 : "Altera Corporation",
0x1173 : "Adobe Systems",
0x1174 : "Bridgeport Machines",
0x1175 : "Mitron Computer Inc.",
0x1176 : "SBE",
0x1177 : "Silicon Engineering",
0x1178 : "Alfa Inc",
0x1179 : "Toshiba corporation",
0x117A : "A-Trend Technology",
0x117B : "LG (Lucky Goldstar) Electronics Inc.",
0x117C : "Atto Technology",
0x117D : "Becton & Dickinson",
0x117E : "T/R Systems",
0x117F : "Integrated Circuit Systems",
0x1180 : "Ricoh",
0x1183 : "Fujikura Ltd",
0x1184 : "Forks Inc",
0x1185 : "Dataworld",
0x1186 : "D-Link System Inc",
0x1187 : "Philips Healthcare",
0x1188 : "Shima Seiki Manufacturing Ltd.",
0x1189 : "Matsushita Electronics",
0x118A : "Hilevel Technology",
0x118B : "Hypertec Pty Ltd",
0x118C : "Corollary Inc",
0x118D : "BitFlow Inc",
0x118E : "Hermstedt AG",
0x118F : "Green Logic",
0x1190 : "Tripace",
0x1191 : "Acard Technology Corp.",
0x1192 : "Densan Co. Ltd",
0x1194 : "Toucan Technology",
0x1195 : "Ratoc System Inc",
0x1196 : "Hytec Electronics Ltd",
0x1197 : "Gage Applied Technologies",
0x1198 : "Lambda Systems Inc",
0x1199 : "Attachmate Corp.",
0x119A : "Mind/Share Inc.",
0x119B : "Omega Micro Inc.",
0x119C : "Information Technology Inst.",
0x119D : "Bug Sapporo Japan",
0x119E : "Fujitsu Microelectronics Ltd.",
0x119F : "Bull Hn Information Systems",
0x11A1 : "Hamamatsu Photonics K.K.",
0x11A2 : "Sierra Research and Technology",
0x11A3 : "Deuretzbacher GmbH & Co. Eng. KG",
0x11A4 : "Barco",
0x11A5 : "MicroUnity Systems Engineering Inc.",
0x11A6 : "Pure Data",
0x11A7 : "Power Computing Corp.",
0x11A8 : "Systech Corp.",
0x11A9 : "InnoSys Inc.",
0x11AA : "Actel",
0x11AB : "Marvell Semiconductor",
0x11AC : "Canon Information Systems",
0x11AD : "Lite-On Technology Corp.",
0x11AE : "Scitex Corporation Ltd",
0x11AF : "Avid Technology, Inc.",
0x11B0 : "Quicklogic Corp",
0x11B1 : "Apricot Computers",
0x11B2 : "Eastman Kodak",
0x11B3 : "Barr Systems Inc.",
0x11B4 : "Leitch Technology International",
0x11B5 : "Radstone Technology Ltd.",
0x11B6 : "United Video Corp",
0x11B7 : "Motorola",
0x11B8 : "Xpoint Technologies Inc",
0x11B9 : "Pathlight Technology Inc.",
0x11BA : "Videotron Corp",
0x11BB : "Pyramid Technology",
0x11BC : "Network Peripherals Inc",
0x11BD : "Pinnacle system",
0x11BE : "International Microcircuits Inc",
0x11BF : "Astrodesign Inc.",
0x11C1 : "LSI Corporation",
0x11C2 : "Sand Microelectronics",
0x11C4 : "Document Technologies Ind.",
0x11C5 : "Shiva Corporatin",
0x11C6 : "Dainippon Screen Mfg. Co",
0x11C7 : "D.C.M. Data Systems",
0x11C8 : "Dolphin Interconnect Solutions",
0x11C9 : "MAGMA",
0x11CA : "LSI Systems Inc",
0x11CB : "Specialix International Ltd.",
0x11CC : "Michels & Kleberhoff Computer GmbH",
0x11CD : "HAL Computer Systems Inc.",
0x11CE : "Primary Rate Inc",
0x11CF : "Pioneer Electronic Corporation",
0x11D0 : "BAE SYSTEMS - Manassas",
0x11D1 : "AuraVision Corporation",
0x11D2 : "Intercom Inc.",
0x11D3 : "Trancell Systems Inc",
0x11D4 : "Analog Devices, Inc.",
0x11D5 : "Tahoma Technology",
0x11D6 : "Tekelec Technologies",
0x11D7 : "TRENTON Technology, Inc.",
0x11D8 : "Image Technologies Development",
0x11D9 : "Tec Corporation",
0x11DA : "Novell",
0x11DB : "Sega Enterprises Ltd",
0x11DC : "Questra Corp",
0x11DD : "Crosfield Electronics Ltd",
0x11DE : "Zoran Corporation",
0x11E1 : "Gec Plessey Semi Inc",
0x11E2 : "Samsung Information Systems America",
0x11E3 : "Quicklogic Corp",
0x11E4 : "Second Wave Inc",
0x11E5 : "IIX Consulting",
0x11E6 : "Mitsui-Zosen System Research",
0x11E8 : "Digital Processing Systems Inc",
0x11E9 : "Highwater Designs Ltd",
0x11EA : "Elsag Bailey",
0x11EB : "Formation, Inc",
0x11EC : "Coreco Inc",
0x11ED : "Mediamatics",
0x11EE : "Dome Imaging Systems Inc",
0x11EF : "Nicolet Technologies BV",
0x11F0 : "Triya",
0x11F2 : "Picture Tel Japan KK",
0x11F3 : "Keithley Instruments, Inc",
0x11F4 : "Kinetic Systems Corporation",
0x11F5 : "Computing Devices Intl",
0x11F6 : "Powermatic Data Systems Ltd",
0x11F7 : "Scientific Atlanta",
0x11F8 : "PMC-Sierra Inc.",
0x11F9 : "I-Cube Inc",
0x11FA : "Kasan Electronics Co Ltd",
0x11FB : "Datel Inc",
0x11FD : "High Street Consultants",
0x11FE : "Comtrol Corp",
0x11FF : "Scion Corp",
0x1200 : "CSS Corp",
0x1201 : "Vista Controls Corp",
0x1202 : "Network General Corp",
0x1203 : "Bayer Corporation Agfa Div",
0x1204 : "Lattice Semiconductor Corp",
0x1205 : "Array Corp",
0x1206 : "Amdahl Corp",
0x1208 : "Parsytec GmbH",
0x1209 : "Sci Systems Inc",
0x120A : "Synaptel",
0x120B : "Adaptive Solutions",
0x120D : "Compression Labs Inc.",
0x120E : "Cyclades Corporation",
0x120F : "Essential Communications",
0x1210 : "Hyperparallel Technologies",
0x1211 : "Braintech Inc",
0x1213 : "Applied Intelligent Systems Inc",
0x1214 : "Performance Technologies Inc",
0x1215 : "Interware Co Ltd",
0x1216 : "Purup-Eskofot A/S",
0x1217 : "O2Micro Inc",
0x1218 : "Hybricon Corp",
0x1219 : "First Virtual Corp",
0x121A : "3dfx Interactive Inc",
0x121B : "Advanced Telecommunications Modules",
0x121C : "Nippon Texa Co Ltd",
0x121D : "LiPPERT Embedded Computers GmbH",
0x121E : "CSPI",
0x121F : "Arcus Technology Inc",
0x1220 : "Ariel Corporation",
0x1221 : "Contec Microelectronics Europe BV",
0x1222 : "Ancor Communications Inc",
0x1223 : "Emerson Network Power, Embedded Computing",
0x1224 : "Interactive Images",
0x1225 : "Power I/O Inc.",
0x1227 : "Tech-Source",
0x1228 : "Norsk Elektro Optikk A/S",
0x1229 : "Data Kinesis Inc.",
0x122A : "Integrated Telecom",
0x122B : "LG Industrial Systems Co. Ltd.",
0x122C : "sci-worx GmbH",
0x122D : "Aztech System Ltd",
0x122E : "Absolute Analysis",
0x122F : "Andrew Corp.",
0x1230 : "Fishcamp Engineering",
0x1231 : "Woodward McCoach Inc.",
0x1233 : "Bus-Tech Inc.",
0x1234 : "Technical Corp",
0x1236 : "Sigma Designs, Inc",
0x1237 : "Alta Technology Corp.",
0x1238 : "Adtran",
0x1239 : "The 3DO Company",
0x123A : "Visicom Laboratories Inc.",
0x123B : "Seeq Technology Inc.",
0x123C : "Century Systems Inc.",
0x123D : "Engineering Design Team Inc.",
0x123F : "C-Cube Microsystems",
0x1240 : "Marathon Technologies Corp.",
0x1241 : "DSC Communications",
0x1242 : "JNI Corporation",
0x1243 : "Delphax",
0x1244 : "AVM AUDIOVISUELLES MKTG & Computer GmbH",
0x1245 : "APD S.A.",
0x1246 : "Dipix Technologies Inc",
0x1247 : "Xylon Research Inc.",
0x1248 : "Central Data Corp.",
0x1249 : "Samsung Electronics Co. Ltd.",
0x124A : "AEG Electrocom GmbH",
0x124C : "Solitron Technologies Inc.",
0x124D : "Stallion Technologies",
0x124E : "Cylink",
0x124F : "Infortrend Technology Inc",
0x1250 : "Hitachi Microcomputer System Ltd.",
0x1251 : "VLSI Solution OY",
0x1253 : "Guzik Technical Enterprises",
0x1254 : "Linear Systems Ltd.",
0x1255 : "Optibase Ltd.",
0x1256 : "Perceptive Solutions Inc.",
0x1257 : "Vertex Networks Inc.",
0x1258 : "Gilbarco Inc.",
0x1259 : "Allied Telesyn International",
0x125A : "ABB Power Systems",
0x125B : "Asix Electronics Corp.",
0x125C : "Aurora Technologies Inc.",
0x125D : "ESS Technology",
0x125E : "Specialvideo Engineering SRL",
0x125F : "Concurrent Technologies Inc.",
0x1260 : "Intersil Corporation",
0x1261 : "Matsushita-Kotobuki Electronics Indu",
0x1262 : "ES Computer Co. Ltd.",
0x1263 : "Sonic Solutions",
0x1264 : "Aval Nagasaki Corp.",
0x1265 : "Casio Computer Co. Ltd.",
0x1266 : "Microdyne Corp.",
0x1267 : "S.A. Telecommunications",
0x1268 : "Tektronix",
0x1269 : "Thomson-CSF/TTM",
0x126A : "Lexmark International Inc.",
0x126B : "Adax Inc.",
0x126C : "Nortel Networks Corp.",
0x126D : "Splash Technology Inc.",
0x126E : "Sumitomo Metal Industries Ltd.",
0x126F : "Silicon Motion",
0x1270 : "Olympus Optical Co. Ltd.",
0x1271 : "GW Instruments",
0x1272 : "Telematics International",
0x1273 : "Hughes Network Systems",
0x1274 : "Ensoniq",
0x1275 : "Network Appliance",
0x1276 : "Switched Network Technologies Inc.",
0x1277 : "Comstream",
0x1278 : "Transtech Parallel Systems",
0x1279 : "Transmeta Corp.",
0x127B : "Pixera Corp",
0x127C : "Crosspoint Solutions Inc.",
0x127D : "Vela Research LP",
0x127E : "Winnov L.P.",
0x127F : "Fujifilm",
0x1280 : "Photoscript Group Ltd.",
0x1281 : "Yokogawa Electronic Corp.",
0x1282 : "Davicom Semiconductor Inc.",
0x1283 : "Waldo",
0x1285 : "Platform Technologies Inc.",
0x1286 : "MAZeT GmbH",
0x1287 : "LuxSonor Inc.",
0x1288 : "Timestep Corp.",
0x1289 : "AVC Technology Inc.",
0x128A : "Asante Technologies Inc.",
0x128B : "Transwitch Corp.",
0x128C : "Retix Corp.",
0x128D : "G2 Networks Inc.",
0x128F : "Tateno Dennou Inc.",
0x1290 : "Sord Computer Corp.",
0x1291 : "NCS Computer Italia",
0x1292 : "Tritech Microelectronics Intl PTE",
0x1293 : "Media Reality Technology",
0x1294 : "Rhetorex Inc.",
0x1295 : "Imagenation Corp.",
0x1296 : "Kofax Image Products",
0x1297 : "Shuttle Computer",
0x1298 : "Spellcaster Telecommunications Inc.",
0x1299 : "Knowledge Technology Laboratories",
0x129A : "Curtiss Wright Controls Electronic Systems",
0x129B : "Image Access",
0x129D : "CompCore Multimedia Inc.",
0x129E : "Victor Co. of Japan Ltd.",
0x129F : "OEC Medical Systems Inc.",
0x12A0 : "Allen Bradley Co.",
0x12A1 : "Simpact Inc",
0x12A2 : "NewGen Systems Corp.",
0x12A3 : "Lucent Technologies AMR",
0x12A4 : "NTT Electronics Corp.",
0x12A5 : "Vision Dynamics Ltd.",
0x12A6 : "Scalable Networks Inc.",
0x12A7 : "AMO GmbH",
0x12A8 : "News Datacom",
0x12A9 : "Xiotech Corp.",
0x12AA : "SDL Communications Inc.",
0x12AB : "Yuan Yuan Enterprise Co. Ltd.",
0x12AC : "MeasureX Corp.",
0x12AD : "MULTIDATA GmbH",
0x12AE : "Alteon Networks Inc.",
0x12AF : "TDK USA Corp.",
0x12B0 : "Jorge Scientific Corp.",
0x12B1 : "GammaLink",
0x12B2 : "General Signal Networks",
0x12B3 : "Interface Corp. Ltd.",
0x12B4 : "Future Tel Inc.",
0x12B5 : "Granite Systems Inc.",
0x12B7 : "Acumen",
0x12B8 : "Korg",
0x12B9 : "3Com Corporation",
0x12BA : "Bittware, Inc",
0x12BB : "Nippon Unisoft Corp.",
0x12BC : "Array Microsystems",
0x12BD : "Computerm Corp.",
0x12BF : "Fujifilm Microdevices",
0x12C0 : "Infimed",
0x12C1 : "GMM Research Corp.",
0x12C2 : "Mentec Ltd.",
0x12C3 : "Holtek Microelectronics Inc.",
0x12C4 : "Connect Tech Inc.",
0x12C5 : "Picture Elements Inc.",
0x12C6 : "Mitani Corp.",
0x12C7 : "Dialogic Corp.",
0x12C8 : "G Force Co. Ltd.",
0x12C9 : "Gigi Operations",
0x12CA : "Integrated Computing Engines, Inc.",
0x12CB : "Antex Electronics Corp.",
0x12CC : "Pluto Technologies International",
0x12CD : "Aims Lab",
0x12CE : "Netspeed Inc.",
0x12CF : "Prophet Systems Inc.",
0x12D0 : "GDE Systems Inc.",
0x12D1 : "Huawei Technologies Co., Ltd.",
0x12D3 : "Vingmed Sound A/S",
0x12D4 : "Ulticom, Inc.",
0x12D5 : "Equator Technologies",
0x12D6 : "Analogic Corp.",
0x12D7 : "Biotronic SRL",
0x12D8 : "Pericom Semiconductor",
0x12D9 : "Aculab Plc.",
0x12DA : "TrueTime",
0x12DB : "Annapolis Micro Systems Inc.",
0x12DC : "Symicron Computer Communication Ltd.",
0x12DD : "Management Graphics Inc.",
0x12DE : "Rainbow Technologies",
0x12DF : "SBS Technologies Inc.",
0x12E0 : "Chase Research PLC",
0x12E1 : "Nintendo Co. Ltd.",
0x12E2 : "Datum Inc. Bancomm-Timing Division",
0x12E3 : "Imation Corp. - Medical Imaging Syst",
0x12E4 : "Brooktrout Technology Inc.",
0x12E6 : "Cirel Systems",
0x12E7 : "Sebring Systems Inc",
0x12E8 : "CRISC Corp.",
0x12E9 : "GE Spacenet",
0x12EB : "Aureal Semiconductor",
0x12EC : "3A International Inc.",
0x12ED : "Optivision Inc.",
0x12EE : "Orange Micro, Inc.",
0x12EF : "Vienna Systems",
0x12F0 : "Pentek",
0x12F1 : "Sorenson Vision Inc.",
0x12F2 : "Gammagraphx Inc.",
0x12F4 : "Megatel",
0x12F5 : "Forks",
0x12F7 : "Cognex",
0x12F8 : "Electronic-Design GmbH",
0x12F9 : "FourFold Technologies",
0x12FB : "Spectrum Signal Processing",
0x12FC : "Capital Equipment Corp",
0x12FE : "esd Electronic System Design GmbH",
0x1303 : "Innovative Integration",
0x1304 : "Juniper Networks Inc.",
0x1307 : "ComputerBoards",
0x1308 : "Jato Technologies Inc.",
0x130A : "Mitsubishi Electric Microcomputer",
0x130B : "Colorgraphic Communications Corp",
0x130F : "Advanet Inc.",
0x1310 : "Gespac",
0x1312 : "Microscan Systems Inc",
0x1313 : "Yaskawa Electric Co.",
0x1316 : "Teradyne Inc.",
0x1317 : "ADMtek Inc",
0x1318 : "Packet Engines, Inc.",
0x1319 : "Forte Media",
0x131F : "SIIG",
0x1325 : "Salix Technologies Inc",
0x1326 : "Seachange International",
0x1328 : "CIFELLI SYSTEMS CORPORATION",
0x1331 : "RadiSys Corporation",
0x1332 : "Curtiss-Wright Controls Embedded Computing",
0x1335 : "Videomail Inc.",
0x133D : "Prisa Networks",
0x133F : "SCM Microsystems",
0x1342 : "Promax Systems Inc",
0x1344 : "Micron Technology, Inc.",
0x1347 : "Spectracom Corporation",
0x134A : "DTC Technology Corp.",
0x134B : "ARK Research Corp.",
0x134C : "Chori Joho System Co. Ltd",
0x134D : "PCTEL Inc.",
0x135A : "Brain Boxes Limited",
0x135B : "Giganet Inc.",
0x135C : "Quatech Inc",
0x135D : "ABB Network Partner AB",
0x135E : "Sealevel Systems Inc.",
0x135F : "I-Data International A-S",
0x1360 : "Meinberg Funkuhren GmbH & Co. KG",
0x1361 : "Soliton Systems K.K.",
0x1363 : "Phoenix Technologies Ltd",
0x1365 : "Hypercope Corp.",
0x1366 : "Teijin Seiki Co. Ltd.",
0x1367 : "Hitachi Zosen Corporation",
0x1368 : "Skyware Corporation",
0x1369 : "Digigram",
0x136B : "Kawasaki Steel Corporation",
0x136C : "Adtek System Science Co Ltd",
0x1375 : "Boeing - Sunnyvale",
0x137A : "Mark Of The Unicorn Inc",
0x137B : "PPT Vision",
0x137C : "Iwatsu Electric Co Ltd",
0x137D : "Dynachip Corporation",
0x137E : "Patriot Scientific Corp.",
0x1380 : "Sanritz Automation Co LTC",
0x1381 : "Brains Co. Ltd",
0x1382 : "Marian - Electronic & Software",
0x1384 : "Stellar Semiconductor Inc",
0x1385 : "Netgear",
0x1387 : "Curtiss-Wright Controls Electronic Systems",
0x1388 : "Hitachi Information Technology Co Ltd",
0x1389 : "Applicom International",
0x138A : "Validity Sensors, Inc.",
0x138B : "Tokimec Inc",
0x138E : "Basler GMBH",
0x138F : "Patapsco Designs Inc",
0x1390 : "Concept Development Inc.",
0x1393 : "Moxa Technologies Co Ltd",
0x1394 : "Level One Communications",
0x1395 : "Ambicom Inc",
0x1396 : "Cipher Systems Inc",
0x1397 : "Cologne Chip Designs GmbH",
0x1398 : "Clarion Co. Ltd",
0x139A : "Alacritech Inc",
0x139D : "Xstreams PLC/ EPL Limited",
0x139E : "Echostar Data Networks",
0x13A0 : "Crystal Group Inc",
0x13A1 : "Kawasaki Heavy Industries Ltd",
0x13A3 : "HI-FN Inc.",
0x13A4 : "Rascom Inc",
0x13A7 : "amc330",
0x13A8 : "Exar Corp.",
0x13A9 : "Siemens Healthcare",
0x13AA : "Nortel Networks - BWA Division",
0x13AF : "T.Sqware",
0x13B1 : "Tamura Corporation",
0x13B4 : "Wellbean Co Inc",
0x13B5 : "ARM Ltd",
0x13B6 : "DLoG Gesellschaft fr elektronische Datentechnik mbH",
0x13B8 : "Nokia Telecommunications OY",
0x13BD : "Sharp Corporation",
0x13BF : "Sharewave Inc",
0x13C0 : "Microgate Corp.",
0x13C1 : "LSI",
0x13C2 : "Technotrend Systemtechnik GMBH",
0x13C3 : "Janz Computer AG",
0x13C7 : "Blue Chip Technology Ltd",
0x13CC : "Metheus Corporation",
0x13CF : "Studio Audio & Video Ltd",
0x13D0 : "B2C2 Inc",
0x13D1 : "AboCom Systems, Inc",
0x13D4 : "Graphics Microsystems Inc",
0x13D6 : "K.I. Technology Co Ltd",
0x13D7 : "Toshiba Engineering Corporation",
0x13D8 : "Phobos Corporation",
0x13D9 : "Apex Inc",
0x13DC : "Netboost Corporation",
0x13DE : "ABB Robotics Products AB",
0x13DF : "E-Tech Inc.",
0x13E0 : "GVC Corporation",
0x13E3 : "Nest Inc",
0x13E4 : "Calculex Inc",
0x13E5 : "Telesoft Design Ltd",
0x13E9 : "Intraserver Technology Inc",
0x13EA : "Dallas Semiconductor",
0x13F0 : "IC Plus Corporation",
0x13F1 : "OCE - Industries S.A.",
0x13F4 : "Troika Networks Inc",
0x13F6 : "C-Media Electronics Inc.",
0x13F9 : "NTT Advanced Technology Corp.",
0x13FA : "Pentland Systems Ltd.",
0x13FB : "Aydin Corp",
0x13FD : "Micro Science Inc",
0x13FE : "Advantech Co., Ltd.",
0x13FF : "Silicon Spice Inc.",
0x1400 : "ArtX Inc",
0x1402 : "Meilhaus Electronic GmbH Germany",
0x1404 : "Fundamental Software Inc",
0x1406 : "Oce Print Logics Technologies S.A.",
0x1407 : "Lava Computer MFG Inc.",
0x1408 : "Aloka Co. Ltd",
0x1409 : "SUNIX Co., Ltd.",
0x140A : "DSP Research Inc",
0x140B : "Ramix Inc",
0x140D : "Matsushita Electric Works Ltd",
0x140F : "Salient Systems Corp",
0x1412 : "IC Ensemble, Inc.",
0x1413 : "Addonics",
0x1415 : "Oxford Semiconductor Ltd - now part of PLX Technology ",
0x1418 : "Kyushu Electronics Systems Inc",
0x1419 : "Excel Switching Corp",
0x141B : "Zoom Telephonics Inc",
0x141E : "Fanuc Co. Ltd",
0x141F : "Visiontech Ltd",
0x1420 : "Psion Dacom PLC",
0x1425 : "Chelsio Communications",
0x1428 : "Edec Co Ltd",
0x1429 : "Unex Technology Corp.",
0x142A : "Kingmax Technology Inc",
0x142B : "Radiolan",
0x142C : "Minton Optic Industry Co Ltd",
0x142D : "Pixstream Inc",
0x1430 : "ITT Aerospace/Communications Division",
0x1433 : "Eltec Elektronik AG",
0x1435 : "RTD Embedded Technologies, Inc.",
0x1436 : "CIS Technology Inc",
0x1437 : "Nissin Inc Co",
0x1438 : "Atmel-Dream",
0x143F : "Lightwell Co Ltd - Zax Division",
0x1441 : "Agie SA.",
0x1443 : "Unibrain S.A.",
0x1445 : "Logical Co Ltd",
0x1446 : "Graphin Co. Ltd",
0x1447 : "Aim GMBH",
0x1448 : "Alesis Studio",
0x144A : "ADLINK Technology Inc",
0x144B : "Loronix Information Systems, Inc.",
0x144D : "sanyo",
0x1450 : "Octave Communications Ind.",
0x1451 : "SP3D Chip Design GMBH",
0x1453 : "Mycom Inc",
0x1458 : "Giga-Byte Technologies",
0x145C : "Cryptek",
0x145F : "Baldor Electric Company",
0x1460 : "Dynarc Inc",
0x1462 : "Micro-Star International Co Ltd",
0x1463 : "Fast Corporation",
0x1464 : "Interactive Circuits & Systems Ltd",
0x1468 : "Ambit Microsystems Corp.",
0x1469 : "Cleveland Motion Controls",
0x146C : "Ruby Tech Corp.",
0x146D : "Tachyon Inc.",
0x146E : "WMS Gaming",
0x1471 : "Integrated Telecom Express Inc",
0x1473 : "Zapex Technologies Inc",
0x1474 : "Doug Carson & Associates",
0x1477 : "Net Insight",
0x1478 : "Diatrend Corporation",
0x147B : "Abit Computer Corp.",
0x147F : "Nihon Unisys Ltd.",
0x1482 : "Isytec - Integrierte Systemtechnik Gmbh",
0x1483 : "Labway Coporation",
0x1485 : "Erma - Electronic GMBH",
0x1489 : "KYE Systems Corporation",
0x148A : "Opto 22",
0x148B : "Innomedialogic Inc.",
0x148C : "C.P. Technology Co. Ltd",
0x148D : "Digicom Systems Inc.",
0x148E : "OSI Plus Corporation",
0x148F : "Plant Equipment Inc.",
0x1490 : "TC Labs Pty Ltd.",
0x1491 : "Futronic ",
0x1493 : "Maker Communications",
0x1495 : "Tokai Communications Industry Co. Ltd",
0x1496 : "Joytech Computer Co. Ltd.",
0x1497 : "SMA Technologie AG",
0x1498 : "Tews Technologies",
0x1499 : "Micro-Technology Co Ltd",
0x149A : "Andor Technology Ltd",
0x149B : "Seiko Instruments Inc",
0x149E : "Mapletree Networks Inc.",
0x149F : "Lectron Co Ltd",
0x14A0 : "Softing GMBH",
0x14A2 : "Millennium Engineering Inc",
0x14A4 : "GVC/BCM Advanced Research",
0x14A9 : "Hivertec Inc.",
0x14AB : "Mentor Graphics Corp.",
0x14B1 : "Nextcom K.K.",
0x14B3 : "Xpeed Inc.",
0x14B4 : "Philips Business Electronics B.V.",
0x14B5 : "Creamware GmbH",
0x14B6 : "Quantum Data Corp.",
0x14B7 : "Proxim Inc.",
0x14B9 : "Aironet Wireless Communication",
0x14BA : "Internix Inc.",
0x14BB : "Semtech Corporation",
0x14BE : "L3 Communications",
0x14C0 : "Compal Electronics, Inc.",
0x14C1 : "Myricom Inc.",
0x14C2 : "DTK Computer",
0x14C4 : "Iwasaki Information Systems Co Ltd",
0x14C5 : "ABB AB (Sweden)",
0x14C6 : "Data Race Inc",
0x14C7 : "Modular Technology Ltd.",
0x14C8 : "Turbocomm Tech Inc",
0x14C9 : "Odin Telesystems Inc",
0x14CB : "Billionton Systems Inc./Cadmus Micro Inc",
0x14CD : "Universal Scientific Ind.",
0x14CF : "TEK Microsystems Inc.",
0x14D4 : "Panacom Technology Corporation",
0x14D5 : "Nitsuko Corporation",
0x14D6 : "Accusys Inc",
0x14D7 : "Hirakawa Hewtech Corp",
0x14D8 : "Hopf Elektronik GMBH",
0x14D9 : "Alpha Processor Inc",
0x14DB : "Avlab Technology Inc.",
0x14DC : "Amplicon Liveline Limited",
0x14DD : "Imodl Inc.",
0x14DE : "Applied Integration Corporation",
0x14E3 : "Amtelco",
0x14E4 : "Broadcom",
0x14EA : "Planex Communications, Inc.",
0x14EB : "Seiko Epson Corporation",
0x14EC : "Acqiris",
0x14ED : "Datakinetics Ltd",
0x14EF : "Carry Computer Eng. Co Ltd",
0x14F1 : "Conexant Systems, Inc. (Formerly Rockwell)",
0x14F2 : "Mobility Electronics, Inc.",
0x14F4 : "Tokyo Electronic Industry Co. Ltd.",
0x14F5 : "Sopac Ltd",
0x14F6 : "Coyote Technologies LLC",
0x14F7 : "Wolf Technology Inc",
0x14F8 : "Audiocodes Inc",
0x14F9 : "AG Communications",
0x14FB : "Transas Marine (UK) Ltd",
0x14FC : "Quadrics Ltd",
0x14FD : "Silex Technology Inc.",
0x14FE : "Archtek Telecom Corp.",
0x14FF : "Twinhead International Corp.",
0x1501 : "Banksoft Canada Ltd",
0x1502 : "Mitsubishi Electric Logistics Support Co",
0x1503 : "Kawasaki LSI USA Inc",
0x1504 : "Kaiser Electronics",
0x1506 : "Chameleon Systems Inc",
0x1507 : "Htec Ltd.",
0x1509 : "First International Computer Inc",
0x150B : "Yamashita Systems Corp",
0x150C : "Kyopal Co Ltd",
0x150D : "Warpspped Inc",
0x150E : "C-Port Corporation",
0x150F : "Intec GMBH",
0x1510 : "Behavior Tech Computer Corp",
0x1511 : "Centillium Technology Corp",
0x1512 : "Rosun Technologies Inc",
0x1513 : "Raychem",
0x1514 : "TFL LAN Inc",
0x1515 : "ICS Advent",
0x1516 : "Myson Technology Inc",
0x1517 : "Echotek Corporation",
0x1518 : "Kontron Modular Computers GmbH (PEP Modular Computers GMBH)",
0x1519 : "Telefon Aktiebolaget LM Ericsson",
0x151A : "Globetek Inc.",
0x151B : "Combox Ltd",
0x151C : "Digital Audio Labs Inc",
0x151D : "Fujitsu Computer Products Of America",
0x151E : "Matrix Corp.",
0x151F : "Topic Semiconductor Corp",
0x1520 : "Chaplet System Inc",
0x1521 : "Bell Corporation",
0x1522 : "Mainpine Limited",
0x1523 : "Music Semiconductors",
0x1524 : "ENE Technology Inc",
0x1525 : "Impact Technologies",
0x1526 : "ISS Inc",
0x1527 : "Solectron",
0x1528 : "Acksys",
0x1529 : "American Microsystems Inc",
0x152A : "Quickturn Design Systems",
0x152B : "Flytech Technology Co Ltd",
0x152C : "Macraigor Systems LLC",
0x152D : "Quanta Computer Inc",
0x152E : "Melec Inc",
0x152F : "Philips - Crypto",
0x1532 : "Echelon Corporation",
0x1533 : "Baltimore",
0x1534 : "Road Corporation",
0x1535 : "Evergreen Technologies Inc",
0x1537 : "Datalex Communcations",
0x1538 : "Aralion Inc.",
0x1539 : "Atelier Informatiques et Electronique Et",
0x153A : "ONO Sokki",
0x153B : "Terratec Electronic GMBH",
0x153C : "Antal Electronic",
0x153D : "Filanet Corporation",
0x153E : "Techwell Inc",
0x153F : "MIPS Technologies, Inc",
0x1540 : "Provideo Multimedia Co Ltd",
0x1541 : "Telocity Inc.",
0x1542 : "Vivid Technology Inc",
0x1543 : "Silicon Laboratories",
0x1544 : "DCM Technologies Ltd.",
0x1545 : "VisionTek",
0x1546 : "IOI Technology Corp.",
0x1547 : "Mitutoyo Corporation",
0x1548 : "Jet Propulsion Laboratory",
0x1549 : "Interconnect Systems Solutions",
0x154A : "Max Technologies Inc.",
0x154B : "Computex Co Ltd",
0x154C : "Visual Technology Inc.",
0x154D : "PAN International Industrial Corp",
0x154E : "Servotest Ltd",
0x154F : "Stratabeam Technology",
0x1550 : "Open Network Co Ltd",
0x1551 : "Smart Electronic Development GMBH",
0x1553 : "Chicony Electronics Co Ltd",
0x1554 : "Prolink Microsystems Corp.",
0x1555 : "Gesytec GmbH",
0x1556 : "PLDA",
0x1557 : "Mediastar Co. Ltd",
0x1558 : "Clevo/Kapok Computer",
0x1559 : "SI Logic Ltd",
0x155A : "Innomedia Inc",
0x155B : "Protac International Corp",
0x155C : "s",
0x155D : "MAC System Co Ltd",
0x155E : "KUKA Roboter GmbH",
0x155F : "Perle Systems Limited",
0x1560 : "Terayon Communications Systems",
0x1561 : "Viewgraphics Inc",
0x1562 : "Symbol Technologies, Inc.",
0x1563 : "A-Trend Technology Co Ltd",
0x1564 : "Yamakatsu Electronics Industry Co Ltd",
0x1565 : "Biostar Microtech Intl Corp",
0x1566 : "Ardent Technologies Inc",
0x1567 : "Jungsoft",
0x1568 : "DDK Electronics Inc",
0x1569 : "Palit Microsystems Inc",
0x156A : "Avtec Systems Inc",
0x156B : "S2io Inc",
0x156C : "Vidac Electronics GMBH",
0x156D : "Alpha-Top Corp",
0x156E : "Alfa Inc.",
0x156F : "M-Systems Flash Disk Pioneers Ltd",
0x1570 : "Lecroy Corporation",
0x1571 : "Contemporary Controls",
0x1572 : "Otis Elevator Company",
0x1573 : "Lattice - Vantis",
0x1574 : "Fairchild Semiconductor",
0x1575 : "Voltaire Advanced Data Security Ltd",
0x1576 : "Viewcast Com",
0x1578 : "Hitt",
0x1579 : "Dual Technology Corporation",
0x157A : "Japan Elecronics Ind. Inc",
0x157B : "Star Multimedia Corp.",
0x157C : "Eurosoft (UK)",
0x157D : "Gemflex Networks",
0x157E : "Transition Networks",
0x157F : "PX Instruments Technology Ltd",
0x1580 : "Primex Aerospace Co.",
0x1581 : "SEH Computertechnik GMBH",
0x1582 : "Cytec Corporation",
0x1583 : "Inet Technologies Inc",
0x1584 : "Uniwill Computer Corporation",
0x1585 : "Marconi Commerce Systems SRL",
0x1586 : "Lancast Inc",
0x1587 : "Konica Corporation",
0x1588 : "Solidum Systems Corp",
0x1589 : "Atlantek Microsystems Pty Ltd",
0x158A : "Digalog Systems Inc",
0x158B : "Allied Data Technologies",
0x158C : "Hitachi Semiconductor & Devices Sales Co",
0x158D : "Point Multimedia Systems",
0x158E : "Lara Technology Inc",
0x158F : "Ditect Coop",
0x1590 : "3pardata Inc.",
0x1591 : "ARN",
0x1592 : "Syba Tech Ltd.",
0x1593 : "Bops Inc",
0x1594 : "Netgame Ltd",
0x1595 : "Diva Systems Corp.",
0x1596 : "Folsom Research Inc",
0x1597 : "Memec Design Services",
0x1598 : "Granite Microsystems",
0x1599 : "Delta Electronics Inc",
0x159A : "General Instrument",
0x159B : "Faraday Technology Corp",
0x159C : "Stratus Computer Systems",
0x159D : "Ningbo Harrison Electronics Co Ltd",
0x159E : "A-Max Technology Co Ltd",
0x159F : "Galea Network Security",
0x15A0 : "Compumaster SRL",
0x15A1 : "Geocast Network Systems Inc",
0x15A2 : "Catalyst Enterprises Inc",
0x15A3 : "Italtel",
0x15A4 : "X-Net OY",
0x15A5 : "Toyota MACS Inc",
0x15A6 : "Sunlight Ultrasound Technologies Ltd",
0x15A7 : "SSE Telecom Inc",
0x15A8 : "Shanghai Communications Technologies Cen",
0x15AA : "Moreton Bay",
0x15AB : "Bluesteel Networks Inc",
0x15AC : "North Atlantic Instruments",
0x15AD : "VMware Inc.",
0x15AE : "Amersham Pharmacia Biotech",
0x15B0 : "Zoltrix International Limited",
0x15B1 : "Source Technology Inc",
0x15B2 : "Mosaid Technologies Inc.",
0x15B3 : "Mellanox Technology",
0x15B4 : "CCI/Triad",
0x15B5 : "Cimetrics Inc",
0x15B6 : "Texas Memory Systems Inc",
0x15B7 : "Sandisk Corp.",
0x15B8 : "Addi-Data GMBH",
0x15B9 : "Maestro Digital Communications",
0x15BA : "Impacct Technology Corp",
0x15BB : "Portwell Inc",
0x15BC : "Agilent Technologies",
0x15BD : "DFI Inc.",
0x15BE : "Sola Electronics",
0x15BF : "High Tech Computer Corp (HTC)",
0x15C0 : "BVM Limited",
0x15C1 : "Quantel",
0x15C2 : "Newer Technology Inc",
0x15C3 : "Taiwan Mycomp Co Ltd",
0x15C4 : "EVSX Inc",
0x15C5 : "Procomp Informatics Ltd",
0x15C6 : "Technical University Of Budapest",
0x15C7 : "Tateyama System Laboratory Co Ltd",
0x15C8 : "Penta Media Co. Ltd",
0x15C9 : "Serome Technology Inc",
0x15CA : "Bitboys OY",
0x15CB : "AG Electronics Ltd",
0x15CC : "Hotrail Inc.",
0x15CD : "Dreamtech Co Ltd",
0x15CE : "Genrad Inc.",
0x15CF : "Hilscher GMBH",
0x15D1 : "Infineon Technologies AG",
0x15D2 : "FIC (First International Computer Inc)",
0x15D3 : "NDS Technologies Israel Ltd",
0x15D4 : "Iwill Corporation",
0x15D5 : "Tatung Co.",
0x15D6 : "Entridia Corporation",
0x15D7 : "Rockwell-Collins Inc",
0x15D8 : "Cybernetics Technology Co Ltd",
0x15D9 : "Super Micro Computer Inc",
0x15DA : "Cyberfirm Inc.",
0x15DB : "Applied Computing Systems Inc.",
0x15DC : "Litronic Inc.",
0x15DD : "Sigmatel Inc.",
0x15DE : "Malleable Technologies Inc",
0x15E0 : "Cacheflow Inc",
0x15E1 : "Voice Technologies Group",
0x15E2 : "Quicknet Technologies Inc",
0x15E3 : "Networth Technologies Inc",
0x15E4 : "VSN Systemen BV",
0x15E5 : "Valley Technologies Inc",
0x15E6 : "Agere Inc.",
0x15E7 : "GET Engineering Corp.",
0x15E8 : "National Datacomm Corp.",
0x15E9 : "Pacific Digital Corp.",
0x15EA : "Tokyo Denshi Sekei K.K.",
0x15EB : "Drsearch GMBH",
0x15EC : "Beckhoff Automation GmbH",
0x15ED : "Macrolink Inc",
0x15EE : "IN Win Development Inc.",
0x15EF : "Intelligent Paradigm Inc",
0x15F0 : "B-Tree Systems Inc",
0x15F1 : "Times N Systems Inc",
0x15F2 : "SPOT Imaging Solutions a division of Diagnostic Instruments, Inc",
0x15F3 : "Digitmedia Corp.",
0x15F4 : "Valuesoft",
0x15F5 : "Power Micro Research",
0x15F6 : "Extreme Packet Device Inc",
0x15F7 : "Banctec",
0x15F8 : "Koga Electronics Co",
0x15F9 : "Zenith Electronics Co",
0x15FA : "Axzam Corporation",
0x15FB : "Zilog Inc.",
0x15FC : "Techsan Electronics Co Ltd",
0x15FD : "N-Cubed.Net",
0x15FE : "Kinpo Electronics Inc",
0x15FF : "Fastpoint Technologies Inc.",
0x1600 : "Northrop Grumman - Canada Ltd",
0x1601 : "Tenta Technology",
0x1602 : "Prosys-TEC Inc.",
0x1603 : "Nokia Wireless Business Communications",
0x1604 : "Central System Research Co Ltd",
0x1605 : "Pairgain Technologies",
0x1606 : "Europop AG",
0x1607 : "Lava Semiconductor Manufacturing Inc.",
0x1608 : "Automated Wagering International",
0x1609 : "Sciemetric Instruments Inc",
0x160A : "Kollmorgen Servotronix",
0x160B : "Onkyo Corp.",
0x160C : "Oregon Micro Systems Inc.",
0x160D : "Aaeon Electronics Inc",
0x160E : "CML Emergency Services",
0x160F : "ITEC Co Ltd",
0x1610 : "Tottori Sanyo Electric Co Ltd",
0x1611 : "Bel Fuse Inc.",
0x1612 : "Telesynergy Research Inc.",
0x1613 : "System Craft Inc.",
0x1614 : "Jace Tech Inc.",
0x1615 : "Equus Computer Systems Inc",
0x1616 : "Iotech Inc.",
0x1617 : "Rapidstream Inc",
0x1618 : "Esec SA",
0x1619 : "FarSite Communications Limited",
0x161B : "Mobilian Israel Ltd",
0x161C : "Berkshire Products",
0x161D : "Gatec",
0x161E : "Kyoei Sangyo Co Ltd",
0x161F : "Arima Computer Corporation",
0x1620 : "Sigmacom Co Ltd",
0x1621 : "Lynx Studio Technology Inc",
0x1622 : "Nokia Home Communications",
0x1623 : "KRF Tech Ltd",
0x1624 : "CE Infosys GMBH",
0x1625 : "Warp Nine Engineering",
0x1626 : "TDK Semiconductor Corp.",
0x1627 : "BCom Electronics Inc",
0x1629 : "Kongsberg Spacetec a.s.",
0x162A : "Sejin Computerland Co Ltd",
0x162B : "Shanghai Bell Company Limited",
0x162C : "C&H Technologies Inc",
0x162D : "Reprosoft Co Ltd",
0x162E : "Margi Systems Inc",
0x162F : "Rohde & Schwarz GMBH & Co KG",
0x1630 : "Sky Computers Inc",
0x1631 : "NEC Computer International",
0x1632 : "Verisys Inc",
0x1633 : "Adac Corporation",
0x1634 : "Visionglobal Network Corp.",
0x1635 : "Decros / S.ICZ a.s.",
0x1636 : "Jean Company Ltd",
0x1637 : "NSI",
0x1638 : "Eumitcom Technology Inc",
0x163A : "Air Prime Inc",
0x163B : "Glotrex Co Ltd",
0x163C : "intel",
0x163D : "Heidelberg Digital LLC",
0x163E : "3dpower",
0x163F : "Renishaw PLC",
0x1640 : "Intelliworxx Inc",
0x1641 : "MKNet Corporation",
0x1642 : "Bitland",
0x1643 : "Hajime Industries Ltd",
0x1644 : "Western Avionics Ltd",
0x1645 : "Quick-Serv. Computer Co. Ltd",
0x1646 : "Nippon Systemware Co Ltd",
0x1647 : "Hertz Systemtechnik GMBH",
0x1648 : "MeltDown Systems LLC",
0x1649 : "Jupiter Systems",
0x164A : "Aiwa Co. Ltd",
0x164C : "Department Of Defense",
0x164D : "Ishoni Networks",
0x164E : "Micrel Inc.",
0x164F : "Datavoice (Pty) Ltd.",
0x1650 : "Admore Technology Inc.",
0x1651 : "Chaparral Network Storage",
0x1652 : "Spectrum Digital Inc.",
0x1653 : "Nature Worldwide Technology Corp",
0x1654 : "Sonicwall Inc",
0x1655 : "Dazzle Multimedia Inc.",
0x1656 : "Insyde Software Corp",
0x1657 : "Brocade Communications Systems",
0x1658 : "Med Associates Inc.",
0x1659 : "Shiba Denshi Systems Inc.",
0x165A : "Epix Inc.",
0x165B : "Real-Time Digital Inc.",
0x165C : "Kondo Kagaku",
0x165D : "Hsing Tech. Enterprise Co. Ltd.",
0x165E : "Hyunju Computer Co. Ltd.",
0x165F : "Comartsystem Korea",
0x1660 : "Network Security Technologies Inc. (NetSec)",
0x1661 : "Worldspace Corp.",
0x1662 : "Int Labs",
0x1663 : "Elmec Inc. Ltd.",
0x1664 : "Fastfame Technology Co. Ltd.",
0x1665 : "Edax Inc.",
0x1666 : "Norpak Corporation",
0x1667 : "CoSystems Inc.",
0x1668 : "Actiontec Electronics Inc.",
0x166A : "Komatsu Ltd.",
0x166B : "Supernet Inc.",
0x166C : "Shade Ltd.",
0x166D : "Sibyte Inc.",
0x166E : "Schneider Automation Inc.",
0x166F : "Televox Software Inc.",
0x1670 : "Rearden Steel",
0x1671 : "Atan Technology Inc.",
0x1672 : "Unitec Co. Ltd.",
0x1673 : "pctel",
0x1675 : "Square Wave Technology",
0x1676 : "Emachines Inc.",
0x1677 : "Bernecker + Rainer",
0x1678 : "INH Semiconductor",
0x1679 : "Tokyo Electron Device Ltd.",
0x167F : "iba AG",
0x1680 : "Dunti Corp.",
0x1681 : "Hercules",
0x1682 : "PINE Technology, Ltd.",
0x1688 : "CastleNet Technology Inc.",
0x168A : "Utimaco Safeware AG",
0x168B : "Circut Assembly Corp.",
0x168C : "Atheros Communications Inc.",
0x168D : "NMI Electronics Ltd.",
0x168E : "Hyundai MultiCAV Computer Co. Ltd.",
0x168F : "KDS Innotech Corp.",
0x1690 : "NetContinuum, Inc.",
0x1693 : "FERMA",
0x1695 : "EPoX Computer Co., Ltd.",
0x16AE : "SafeNet Inc.",
0x16B3 : "CNF Mobile Solutions",
0x16B8 : "Sonnet Technologies, Inc.",
0x16CA : "Cenatek Inc.",
0x16CB : "Minolta Co. Ltd.",
0x16CC : "Inari Inc.",
0x16D0 : "Systemax",
0x16E0 : "Third Millenium Test Solutions, Inc.",
0x16E5 : "Intellon Corporation",
0x16EC : "U.S. Robotics",
0x16F0 : "LaserLinc Inc.",
0x16F1 : "Adicti Corp.",
0x16F3 : "Jetway Information Co., Ltd",
0x16F6 : "VideoTele.com Inc.",
0x1700 : "Antara LLC",
0x1701 : "Interactive Computer Products Inc.",
0x1702 : "Internet Machines Corp.",
0x1703 : "Desana Systems",
0x1704 : "Clearwater Networks",
0x1705 : "Digital First",
0x1706 : "Pacific Broadband Communications",
0x1707 : "Cogency Semiconductor Inc.",
0x1708 : "Harris Corp.",
0x1709 : "Zarlink Semiconductor",
0x170A : "Alpine Electronics Inc.",
0x170B : "NetOctave Inc.",
0x170C : "YottaYotta Inc.",
0x170D : "SensoMotoric Instruments GmbH",
0x170E : "San Valley Systems, Inc.",
0x170F : "Cyberdyne Inc.",
0x1710 : "Pelago Nutworks",
0x1711 : "MyName Technologies, Inc.",
0x1712 : "NICE Systems Inc.",
0x1713 : "TOPCON Corp.",
0x1725 : "Vitesse Semiconductor",
0x1734 : "Fujitsu-Siemens Computers GmbH",
0x1737 : "LinkSys",
0x173B : "Altima Communications Inc.",
0x1743 : "Peppercon AG",
0x174B : "PC Partner Limited",
0x1752 : "Global Brands Manufacture Ltd.",
0x1753 : "TeraRecon, Inc.",
0x1755 : "Alchemy Semiconductor Inc.",
0x176A : "General Dynamics Canada",
0x1775 : "General Electric",
0x1789 : "Ennyah Technologies Corp",
0x1793 : "Unitech Electronics Co., Ltd",
0x17A1 : "Tascorp",
0x17A7 : "Start Network Technology Co., Ltd.",
0x17AA : "Legend Ltd. (Beijing)",
0x17AB : "Phillips Components",
0x17AF : "Hightech Information Systems, Ltd.",
0x17BE : "Philips Semiconductors",
0x17C0 : "Wistron Corp.",
0x17C4 : "Movita",
0x17CC : "NetChip",
0x17cd : "Cadence Design Systems",
0x17D5 : "Neterion Inc.",
0x17db : "Cray, Inc.",
0x17E9 : "DH electronics GmbH / Sabrent",
0x17EE : "Connect Components, Ltd.",
0x17F3 : "RDC Semiconductor Co., Ltd.",
0x17FE : "INPROCOMM",
0x1813 : "Ambient Technologies Inc",
0x1814 : "Ralink Technology, Corp.",
0x1815 : "devolo AG",
0x1820 : "InfiniCon Systems, Inc.",
0x1824 : "Avocent",
0x1841 : "Panda Platinum",
0x1860 : "Primagraphics Ltd.",
0x186C : "Humusoft S.R.O",
0x1887 : "Elan Digital Systems Ltd",
0x1888 : "Varisys Limited",
0x188D : "Millogic Ltd.",
0x1890 : "Egenera, Inc.",
0x18BC : "Info-Tek Corp.",
0x18C9 : "ARVOO Engineering BV",
0x18CA : "XGI Technology Inc",
0x18F1 : "Spectrum Systementwicklung Microelectronic GmbH",
0x18F4 : "Napatech A/S",
0x18F7 : "Commtech, Inc.",
0x18FB : "Resilience Corporation",
0x1904 : "Ritmo",
0x1905 : "WIS Technology, Inc.",
0x1910 : "Seaway Networks",
0x1912 : "usb 3.0 Renesas Electronics",
0x1931 : "Option NV",
0x1941 : "Stelar",
0x1954 : "One Stop Systems, Inc.",
0x1969 : "Atheros Communications",
0x1971 : "AGEIA Technologies, Inc.",
0x197B : "JMicron Technology Corp.",
0x198a : "Nallatech",
0x1991 : "Topstar Digital Technologies Co., Ltd.",
0x19a2 : "ServerEngines",
0x19A8 : "DAQDATA GmbH",
0x19AC : "Kasten Chase Applied Research",
0x19B6 : "Mikrotik",
0x19E2 : "Vector Informatik GmbH",
0x19E3 : "DDRdrive LLC",
0x1A08 : "Linux Networx",
0x1a41 : "Tilera Corporation",
0x1A42 : "Imaginant",
0x1B13 : "Jaton Corporation USA",
0x1B21 : "Asustek - ASMedia Technology Inc.",
0x1B6F : "Etron",
0x1B73 : "Fresco Logic Inc.",
0x1B91 : "Averna",
0x1BAD : "ReFLEX CES",
0x1C0F : "Monarch Innovative Technologies Pvt Ltd's ",
0x1C32 : "Highland Technology, Inc.",
0x1c39 : "Thomson Video Networks",
0x1DE1 : "Tekram",
0x1FCF : "Miranda Technologies Ltd.",
0x2001 : "Temporal Research Ltd",
0x2646 : "Kingston Technology Co.",
0x270F : "ChainTek Computer Co. Ltd.",
0x2EC1 : "Zenic Inc",
0x3388 : "Hint Corp.",
0x3411 : "Quantum Designs (H.K.) Inc.",
0x3513 : "ARCOM Control Systems Ltd.",
0x38EF : "4links",
0x3D3D : "3Dlabs, Inc. Ltd",
0x4005 : "Avance Logic Inc.",
0x4144 : "Alpha Data",
0x416C : "Aladdin Knowledge Systems",
0x4348 : "wch.cn",
0x4680 : "UMAX Computer Corp.",
0x4843 : "Hercules Computer Technology",
0x4943 : "Growth Networks",
0x4954 : "Integral Technologies",
0x4978 : "Axil Computer Inc.",
0x4C48 : "Lung Hwa Electronics",
0x4C53 : "SBS-OR Industrial Computers",
0x4CA1 : "Seanix Technology Inc",
0x4D51 : "Mediaq Inc.",
0x4D54 : "Microtechnica Co Ltd",
0x4DDC : "ILC Data Device Corp.",
0x4E8 : "Samsung Windows Portable Devices",
0x5053 : "TBS/Voyetra Technologies",
0x508A : "Samsung T10 MP3 Player",
0x5136 : "S S Technologies",
0x5143 : "Qualcomm Inc. USA",
0x5333 : "S3 Graphics Co., Ltd",
0x544C : "Teralogic Inc",
0x5555 : "Genroco Inc.",
0x5853 : "Citrix Systems, Inc.",
0x6409 : "Logitec Corp.",
0x6666 : "Decision Computer International Co.",
0x6945 : "ASMedia Technology Inc.",
0x7604 : "O.N. Electric Co. Ltd.",
0x7d1 : "D-Link Corporation",
0x8080 : "Xirlink, Inc",
0x8086 : "Intel Corporation",
0x8087 : "Intel",
0x80EE : "Oracle Corporation - InnoTek Systemberatung GmbH",
0x8866 : "T-Square Design Inc.",
0x8888 : "Silicon Magic",
0x8E0E : "Computone Corporation",
0x9004 : "Adaptec Inc",
0x9005 : "Adaptec Inc",
0x919A : "Gigapixel Corp",
0x9412 : "Holtek",
0x9699 : "Omni Media Technology Inc.",
0x9710 : "MosChip Semiconductor Technology",
0x9902 : "StarGen, Inc.",
0xA0A0 : "Aopen Inc.",
0xA0F1 : "Unisys Corporation",
0xA200 : "NEC Corp.",
0xA259 : "Hewlett Packard",
0xA304 : "Sony",
0xA727 : "3com Corporation",
0xAA42 : "Scitex Digital Video",
0xAC1E : "Digital Receiver Technology Inc",
0xB1B3 : "Shiva Europe Ltd.",
0xB894 : "Brown & Sharpe Mfg. Co.",
0xBEEF : "Mindstream Computing",
0xC001 : "TSI Telsys",
0xC0A9 : "Micron/Crucial Technology",
0xC0DE : "Motorola",
0xC0FE : "Motion Engineering Inc.",
0xC622 : "Hudson Soft Co Ltd",
0xCA50 : "Varian, Inc",
0xCAFE : "Chrysalis-ITS",
0xCCCC : "Catapult Communications",
0xD4D4 : "Curtiss-Wright Controls Embedded Computing",
0xDC93 : "Dawicontrol",
0xDEAD : "Indigita Corporation",
0xDEAF : "Middle Digital, Inc",
0xE159 : "Tiger Jet Network Inc",
0xE4BF : "EKF Elektronik GMBH",
0xEA01 : "Eagle Technology",
0xEABB : "Aashima Technology B.V.",
0xEACE : "Endace Measurement Systems Ltd.",
0xECC0 : "Echo Digital Audio Corporation",
0xEDD8 : "ARK Logic, Inc",
0xF5F5 : "F5 Networks Inc.",
0xFA57 : "Interagon AS",
}
DEVICES = {
0x0033 : { 0x002F : "ieee 1394 controller",
0x0033 : "1ACPIGenuineIntel_-_x86_Family_6_Model_23_0",
},
0x003D : { 0x003d : "1740pci",
0x00D1 : "i740 PCI",
},
0x0070 : { 0x6800 : "Hauppage Nova -TD-500 DVB-T Tuner Device",
0x6800 : "Hauppage Nova -TD-500 DVB-T Tuner Device",
},
0x0402 : { 0x5606 : "0x2592",
0x9665 : " ZCT8YBT",
},
0x046D : { 0x0805 : "n.a.",
0x0808 : "Logitech Webcam C600",
0x0809 : "Webcam Pro 9000",
0x082B : "n/a",
0x0896 : "Camera",
0x08AD : "Quickcam Communicate STX",
0x08AF : "-",
0x08b2 : "logitech QuickCam Pro 4000",
0x08C6 : "Logitech OEM Webcam",
0x08f0 : "n/a",
0x08F6 : "QuickCam Communicate",
0x092F : "model number: V-UAP9",
0x0A0B : "Logitech ClearChat Pro USB",
0x0A1F : "Logitech G930 Headset",
0x5a61 : "",
0xC018 : "Baesline 3 Button Corded Optical Mouse",
0xC045 : "Epoxy Hidden",
0xC046 : "n/a",
0xc05b : "ftht",
0xC063 : "DELL 6-Button mouse",
0xC226 : "n/a",
0xC227 : "n/a",
0xC281 : "Wingman Force J-UA9",
0xC312 : "n/a",
0xC404 : "Logitech TrackMan Wheel",
0xC50E : " C-BS35",
0xC512 : "n/a",
0xc51e : "Unknown",
0xC526 : "n/a",
0xC52A : "HID Keyboard Device",
0xC52B : "N/A",
0xC52E : "USB3 receiver",
},
0x0483 : { 0x2016 : "Driver Windows 7",
},
0x04B3 : { 0x24D5 : "Audio Controller",
0x401 : "PCIVEN_8086&DEV_293E&SUBSYS_20F217AA&REV_033&B1BFB68&0&D8 ",
0x401 : "PCIVEN_8086&DEV_24C5&REV_013",
0x4010 : "PCIVEN_8086&DEV_1C22&SUBSYS_FCD01179&REV_04",
0x9876 : "PCIVEN_8086&DEV_293E&SUBSYS_20F217AA&REV_033&B1BFB68&0&D8",
},
0x04D9 : { 0x1603 : "Samsung",
0x2011 : "n/a",
},
0x04F2 : { 0xb008 : ".oem44.inf",
0xB175 : "SN",
0xB307 : "Webcam",
},
0x051D : { 0x0002 : "n/a",
},
0x0553 : { 0x0200 : " Aiptek USA",
},
0x058f : { 0x0001 : "AM usb storage",
0x1234 : "6387",
0x6362 : "Unknown 4-in-1 card reader (istar)",
0x6366 : "Multi Flash Reader USB Device",
0x6387 : "Transcend JetFlash Flash Drive",
0x9254 : "http://www.alldatasheet.com/datasheet-pdf/pdf/91600/ETC/AU9254A21.html",
0x9380 : "Micron=MT29F32G08CBABA",
0x9540 : "SmartCard Reader",
},
0x0590 : { 0x0028 : "hid device class blood pressure monitor",
},
0x05ac : { 0x021e : "Keyboard IT USB",
0x1293 : "Apple iPod",
0x1297 : "Apple iPhone 01 193700 743771 8 ",
0x21e : "keyboard It USB ",
},
0x05E1 : { 0x0408 : "USB 2.0 Video Capture Controller",
0x0501 : "web cam",
},
0x064e : { 0x064e : "Suyin",
0xa101 : "Acer Crystal Eye Webcam",
0xa103 : "WebCam",
0xa116 : "USB 2.0 UVC 1.3M WebCam",
0xA219 : "SUYIN 1.3M WebCam",
0xc108 : "its a webcam software",
0xd101 : "Web Cam",
},
0x067B : { 0x2303 : "Prolific USB 2 Serial Comm Port controller",
0x2305 : "USB-to-Printer Bridge Controller",
0x2393 : "prolific",
0x2506 : "Hi-Speed USB to IDE Bridge Controller",
0x25a1 : "Prolific PCLinq3 USB Transfer Cable Driver",
0x9876 : "TES",
},
0x06FE : { 0x9700 : "a netcard used usb interface",
},
0x093a : { 0x2468 : "http://genius.ru/products.aspx?pnum=24948&archive=1",
0x2608 : "USBVID_093A&PID_2608&REV_0100&MI_00",
0x2620 : "WEBCAM http://www.canyon-tech.com/archive/voip/webcams/CNR-WCAM53#pr-switcher",
},
0x096E : { 0x0201 : " ",
},
0x0A5C : { 0x0201 : "Broadcom USB iLine10(tm) Network Adapter",
0x10DE : "Controlador sm",
0x2000 : "Broadcom Bluetooth Firmware Upgrade Device",
0x2009 : "Broadcom Bluetooth Controller",
0x200a : "Broadcom Bluetooth Controller",
0x200f : "Broadcom Bluetooth Controller",
0x201d : "BROADCOM Bluetooth Device",
0x201e : "IBM Integrated Bluetooth IV",
0x2020 : "Broadcom Bluetooth Dongle",
0x2021 : "BCM2035B3 ROM Adapter Generic",
0x2033 : "Broadcom Blutonium Device Firmware Downloader",
0x2035 : "BCM92035NMD Bluetooth",
0x2038 : "Broadcom Blutonium Device Firmware Downloader (BCM2038)",
0x2039 : "BROADCOM Bluetooth Device",
0x2045 : "Broadcom Bluetooth Controller",
0x2046 : "Broadcom USB Bluetooth Device",
0x2047 : "Broadcom USB Bluetooth Device",
0x205e : "Broadcom Bluetooth Firmware Upgrade Device",
0x2100 : "Broadcom Bluetooth 2.0+eDR USB dongle",
0x2101 : "Broadcom Bluetooth 2.0+EDR USB dongle",
0x2102 : "ANYCOM Blue USB-200/250",
0x2110 : "Broadcom Bluetooth Controller",
0x2111 : "ANYCOM Blue USB-UHE 200/250",
0x2120 : "Broadcom 2045 Bluetooth 2.0 USB-UHE Device with trace filter",
0x2121 : "Broadcom 2045 Bluetooth 2.0 USB Device with trace filter",
0x2122 : "Broadcom Bluetooth 2.0+EDR USB dongle",
0x2124 : "2045B3ROM Bluetooth Dongle",
0x2130 : "Broadcom 2045 Bluetooth 2.0 USB-UHE Device with trace filter",
0x2131 : "Broadcom 2045 Bluetooth 2.0 USB Device with trace filter",
0x2140 : "2046 Flash UHE Class 2",
0x2141 : "2046 Flash non UHE Class 2",
0x2142 : "2046 Flash non UHE Class 1",
0x2143 : "2046 Flash non UHE Class 1",
0x2144 : "2046 Flash non UHE module Class 2",
0x2145 : "Broadcom BCM9204MD LENO Module",
0x2146 : "Broadcom 2045 Bluetooth 2.1 USB UHE Dongle",
0x2147 : "Broadcom 2046 Bluetooth 2.1 USB Dongle",
0x2148 : "Broadcom 2046 Bluetooth 2.1 USB UHE Dongle",
0x2149 : "Broadcom 2046 Bluetooth 2.1 USB Dongle",
0x214a : "Broadcom 2046 Bluetooth 2.1 USB Module",
0x214b : "Broadcom 2046 Bluetooth 2.1 USB Module",
0x214c : "Broadcom 2046 Bluetooth 2.1 USB Module",
0x214d : "Broadcom Bluetooth 2.1 UHE Module",
0x214e : "Thinkpad Bluetooth with Enhanced Data Rate II",
0x214f : "Broadcom 2046 Bluetooth 2.1 USB UHE Dongle",
0x2150 : "Broadcom 2046 Bluetooth 2.1 USB Dongle",
0x2151 : "Broadcom Bluetooth 2.1 USB Dongle",
0x2152 : "Broadcom 2046 Bluetooth 2.1 USB UHE Dongle",
0x2153 : "Broadcom 2046 Bluetooth 2.1 USB UHE Dongle",
0x2154 : "Broadcom 2046 Bluetooth 2.1 USB UHE Dongle",
0x2155 : "Broadcom Bluetooth USB Dongle",
0x2157 : "BCM2046 B1 USB 500",
0x2158 : "Broadcom 2046 Bluetooth 2.1 Device",
0x219C : "Broadcom BCM2070 Bluetooth 3.0+HS USB Device ",
0x21E3 : "Broadcom Bluetooth 4.0",
0x4500 : "Broadcom 2046 Bluetooth 2.1 USB Dongle",
0x4502 : "Broadcom 2046 Bluetooth 2.1 USB Dongle",
0x4503 : "Broadcom 2046 Bluetooth 2.1 USB Dongle",
0x5800 : "Unified Security Hub",
0x5801 : "Unified Security Hub ",
0x6300 : "Pirelli ISB Remote NDIS Device",
0x6688 : "NVIDIA GeForce GT 240M",
0x8613 : "TD 3104 USB vedio grabber ",
0x9876 : "0x9876",
},
0x0A92 : { 0x1010 : "1010&REV_0101&MI_00",
},
0x0AC8 : { 0x1234 : "1",
0x6719 : "asus",
},
0x0b05 : { 0x170C : " RFHID",
},
0x0c45 : { 0x0C45 : "USB2.0",
0x1111 : "USB webcam",
0x5243 : "xda exec Uknown device",
0x6007 : "Genius WebCam Eye",
0x600D : "USB(v1.1) webcam",
0x602C : "Webcam",
0x602D : "USB Webcam",
0x6030 : "USB WebCam ",
0x610C : "usb web camera ",
0x6128 : "USB WebCam",
0x6128 : "USB PC Camera Plus",
0x6129 : "USB WebCam",
0x6130 : "USB HUB",
0x613A : "USB WEBCAM",
0x613c : "USB Webcam",
0x613E : "USB Camera",
0x624f : "Integrated Webcam in Compal HEL81 series barebones.",
0x6270 : "USB Microscopr",
0x6270 : "webcam with mic link works for win 7",
0x6270 : "webcam",
0x627F : "USBVID_17A1&PID_0118&REV_0100",
0x62B3 : "USB 2.0 PC Camera",
0x62BF : "USBVid_0c45&Pid_62bf&Rev_0100",
0x62c0 : "Sonix Wecam",
0x6353 : "USB Microscope",
0x641D : "1.3 MPixel Integrated Webcam used in Dell N5010 series",
0x6421 : "USB 2.0 Webcam slim 32",
0x642F : "Webcam",
0x644b : "not known",
0x6489 : "Integrated Webcam Universal Serial Bus controllers",
0x6840 : "sonix 1.3 mp laptop integrated webcam",
0x9876 : "webcam",
},
0x0cf3 : { 0x1002 : "Wireless USB 2.0 adapter TL-WN821N",
0x3000 : "неизвестное уст&",
0x3002 : "unkown",
0x3002 : "unknown",
0x3005 : "Atheros Bluetooth Module",
0x9271 : "TP-LINK 150 Mbps Wireless Lite N Adapter TL-WN721N",
},
0x0D8C : { 0x0102 : "6206lc",
0x5200 : "0x5200",
},
0x0DF6 : { 0x9071 : "t9071t WL-113 - Wireless Network USB dongle 54g ",
},
0x0E11 : { 0x0001 : "PCI to EISA Bridge",
0x0002 : "PCI to ISA Bridge",
0x000F : "StorageWorks Library Adapter (HVD)",
0x0012 : "686P7",
0x0046 : "Smart Array 6400 Controller",
0x0049 : "Gigabit Upgrade Module",
0x004A : "Gigabit Server Adapter",
0x005A : "HP Remote Insight Lights-Out II Board",
0x00B1 : "HP Remote Insight Lights-Out II PCI Device",
0x00C0 : "64Bit",
0x0508 : "PCI UTP/STP Controller",
0x1000 : "Pentium Bridge",
0x2000 : "Pentium Bridge",
0x3032 : "GUI Accelerator",
0x3033 : "GUI Accelerator",
0x3034 : "GUI Accelerator",
0x4000 : "Pentium Bridge",
0x6010 : "HotPlug PCI Bridge",
0x7020 : "USB Controller",
0xA0EC : "Original Compaq fibre Channel HBA",
0xA0F0 : "Advanced System Management Controller",
0xA0F3 : "Triflex PCI to ISA PnP Bridge",
0xA0F7 : " device 4",
0xA0F8 : "USB Open Host Controller",
0xA0FC : "Tachyon TL 64-bit/66-Mhz FC HBA",
0xAe10 : "Smart-2 Array Controller",
0xAE29 : "PCI to ISA Bridge",
0xAE2A : "CPU to PCI Bridge",
0xAE2B : "PCI to ISA PnP Bridge",
0xAE31 : "System Management Controller",
0xAE32 : "Netelligent 10/100 TX PCI UTP TLAN 2.3",
0xAE33 : "Dual EIDE Controller",
0xAE34 : "Netelligent 10 T PCI UTP TLAN 2.3",
0xAE35 : "Integrated NetFlex 3/P TLAN 2.3",
0xAE40 : "Dual Port Netelligent 10/100 TX PCI TLAN",
0xAE43 : "Integrated Netelligent 10/100 TX PCI",
0xAE69 : "PCI to ISA Bridge",
0xAE6C : "PCI Bridge",
0xAE6D : "CPU to PCI Bridge",
0xB011 : "Dual Port Netelligent 10/100 TX",
0xB012 : "UTP/Coax PCI",
0xB01E : "Fast Ethernet NIC",
0xB01F : "Fast Ethernet NIC",
0xB02F : "Ethernet NIC",
0xB030 : "10/100TX Embedded UTP/Coax Controller",
0xB04A : "10/100TX WOL UTP Controller",
0XB060 : "SMART2 Array Controller",
0xB0C6 : "Fast Ethernet Embedded Controller w/ WOL",
0xB0C7 : "Fast Ethernet NIC",
0xB0D7 : "Fast Ethernet NIC",
0xB0DD : "Fast Ethernet NIC",
0xB0DE : "Fast Ethernet NIC",
0xB0DF : "Gigabit Module",
0xB0E0 : "Gigabit Module",
0xB0E1 : "Fast Ethernet Module",
0xB123 : "Gigabit NIC",
0xB134 : "Fast Ethernet NIC",
0xB13C : "Fast Ethernet NIC",
0xB144 : "Fast Ethernet NIC",
0xB163 : "Fast Ethernet NIC",
0xB164 : "Fast Ethernet Upgrade Module",
0xB178 : "SMART2 Array Controller",
0xB196 : "Conexant SoftK56 Modem",
0xB1A4 : "Gigabit Server Adapter",
0xB203 : "Integrated Lights Out Processor",
0xB204 : "Integrated Lights Out Processor",
0xF095 : "HP StorageWorks 2 Gb",
0xF130 : "ThunderLAN 1.0 NetFlex-3/P",
0xF150 : "ThunderLAN 2.3 NetFlex-3/P with BNC",
0xF700 : "LP7000 Compaq/Emulex Fibre Channel HBA",
0xF800 : "LP8000 Compaq/Emulex Fibre Channel HBA",
},
0x0E8D : { 0x0002 : "PCI Simple Communications Controller",
0x0003 : "usb",
},
0x1000 : { 0x0001 : "PCI-SCSI I/O Processor",
0x0002 : "Fast-wide SCSI gg",
0x0003 : "PCI to SCSI I/O Processor",
0x0004 : "SCSI raid controllers",
0x0005 : "Fast SCSI",
0x0006 : "PCI to Ultra SCSI I/O Processor",
0x000A : "PCI Dual Channel Wide Ultra2 SCSI Ctrlr",
0x000B : "PCI Dual Channel Wide Ultra2 SCSI Ctrlr",
0x000C : "PCI to Ultra2 SCSI I/O Processor",
0x000D : "Ultra Wide SCSI",
0x000F : "PCI to Ultra SCSI I/O Processor",
0x0010 : "I2O-Ready PCI RAID Ultra2 SCSI Ctrlr",
0x0012 : "PCI to Ultra2 SCSI Controller",
0x0013 : "PCI to Ultra SCSI Controller",
0x0020 : "PCI to Dual Channel Ultra3 SCSI Ctrlr",
0x0021 : "PCI to Ultra160 SCSI Controller",
0x0030 : "PCI-X to Ultra320 SCSI Controller",
0x0031 : "PCI-X SCSI Controller",
0x0032 : "PCI-X to Ultra320 SCSI Controller",
0x0035 : "PCI-X SCSI Controller",
0x0040 : "PCI-X to Ultra320 SCSI Controller",
0x0050 : "LSISAS1068E / LSI SAS 6i RAID Controller",
0x0054 : "PCI-X Fusion-MPT SAS",
0x0056 : "PCI-Express Fusion-MPT SAS",
0x0058 : "PCI-Express Fusion-MPT SAS",
0x005e : "PCI-X Fusion-MPT SAS",
0x0060 : "0x10f9",
0x0062 : "PCI-Express Fusion-MPT SAS",
0x0064 : "PCI-Express Fusion-MPT SAS 2.0",
0x0072 : "Dell PERC H200",
0x0073 : "IBM ServeRAID M1015",
0x008F : "LSI 53C8xx SCSI host adapter chip",
0x0408 : "U320-2E Raid Controller",
0x0621 : "Fibre Channel I/O Processor",
0x0622 : "Dial Channel Fibre Channel I/O Processor",
0x0623 : "Dual Channel Fibre Channel I/O Processor",
0x0624 : "Fibre Channel I/O Processor",
0x0625 : "Fibre Channel I/O Processor",
0x0626 : "Fibre Channel Adapter",
0x0628 : "Fibre Channel Adapter",
0x0630 : "Fibre Channel I/O Processor",
0x0640 : "Fibre Channel Adapter",
0x0642 : "Fibre Channel Adapter",
0x0646 : "Fibre Channel Adapter",
0x0701 : "10/100 MBit Ethernet",
0x0702 : "Gigabit Ethernet Controller",
0x0901 : "USB Controller",
0x1000 : "Fast SCSI Controller",
0x1001 : "Symbios Ultra2 SCSI controller",
0x1010 : "Single channel SCSI controller",
0x1020 : "LSI Logic MegaRAID 320-1 Dell PowerEdge PERC 4/SC",
0x1960 : "RAID Controller",
0x9876 : "5946504E44383243",
},
0x1001 : { 0x0010 : "PCI 1616",
0x0011 : "OPTO-PCI",
0x0012 : "PCI-AD",
0x0013 : "PCI-OptoRel",
0x0014 : "Timer",
0x0015 : "PCI-DAC416",
0x0016 : "PCI-MFB high-speed analog I/O",
0x0017 : "PROTO-3 PCI",
0x0020 : "Universal digital I/O PCI-Interface",
},
0x1002 : { 0x4370 : "RV370",
0x0000 : "{4D36E968-E325-11CE-BFC1-08002BE10318}",
0x0002 : "EMU10K1",
0x000D : "bhjkh",
0x0180 : "LXPAY0Y001926158A92000 ",
0x0300 : "1002",
0x0B12 : "R580",
0x1002 : "0F2A1787",
0x1002 : "RV360",
0x1043 : "RV410",
0x11 : "0x215r2qzua21",
0x1111 : "ATI Technologies Inc. / Advanced Micro Devices",
0x1714 : "A4-3400",
0x1ab8 : "2",
0x3150 : "M24",
0x3151 : "RV380",
0x3152 : "M24",
0x3154 : "M24GL",
0x3171 : "RV380",
0x3E50 : "PCIVEN_1002&DEV_3E50&SUBSYS_0410174B&REV_004&243",
0x3E54 : "RV380GL",
0x3E70 : "RV380",
0x3E74 : "RV380GL",
0x4136 : "A3",
0x4137 : "RS200",
0x4143 : "9550",
0x4144 : "R300",
0x4145 : "R300",
0x4146 : "R300",
0x4147 : "R300GL",
0x4148 : "R350",
0x4149 : "R350",
0x4150 : "RV350",
0x4151 : "RV350",
0x4152 : "RV360",
0x4153 : "RV350",
0x4154 : "RV350GL",
0x4155 : "RV350",
0x4158 : "0x5954",
0x4164 : "R300",
0x4166 : "R300",
0x4167 : "R300GL",
0x4168 : "R350",
0x4169 : "R350",
0x4170 : "RV350",
0x4171 : "RV350",
0x4172 : "REV_00",
0x4173 : "RV350",
0x4174 : "RV350GL",
0x4175 : "RV350",
0x4242 : "R200AIW",
0x4243 : "",
0x4336 : "rs200",
0x4337 : "RS200M",
0x4341 : "SB200",
0x4342 : "SB200",
0x4345 : "SB200",
0x4347 : "SB200",
0x4348 : "SB200",
0x4349 : "SB200",
0x434C : "SB200",
0x434d : "SB200",
0x4353 : "SB200",
0x4354 : "215CT",
0x4358 : "210888CX",
0x4361 : "ALC665",
0x4363 : "SB300",
0x4369 : "IXP 3xx",
0x436E : "IXP 3xx",
0x4370 : "SB400",
0x4371 : "IXP SB400",
0x4372 : "SMBus Controller",
0x4373 : "IXP SB400",
0x4374 : "IXP SB400",
0x4375 : "IXP SB400",
0x4376 : "SB4xx",
0x4377 : "IXP SB400",
0x4378 : "SB400",
0x4379 : "SB400 / SB450 (Sil3112)",
0x437A : "SB4xx",
0x437B : "SB450",
0x4380 : "ATI SB600",
0x4380 : "ATI SB600",
0x4380 : "ATI RS690m",
0x4381 : "ATI ?",
0x4383 : "SB700",
0x4385 : "ATI RD600/RS600",
0x4386 : "690G",
0x438C : "RD600/RS600",
0x438D : "SB600",
0x439 : "rv360",
0x4390 : "SB750",
0x4391 : "ATI SB700",
0x4391 : "9H54474G00579",
0x4392 : "ATI SB700",
0x4393 : "ATI SB850",
0x4394 : "5100",
0x4396 : "210888CX",
0x4398 : "SB700",
0x439C : "SB7xx",
0x439D : "SB700 LPC",
0x4437 : "ATI Mobility Radeon 7000 IGP",
0x4554 : "Mach64 ET",
0x4654 : "Mach64 VT",
0x4742 : "(GT-C2U2)",
0x4744 : "Rage 3D Pro AGP 2x",
0x4747 : "GT-C2U2",
0x4749 : "RAGE PRO TURBO AGP 2X",
0x474C : "Rage XC PCI-66",
0x474D : "Rage XL AGP 2x",
0x474E : "Rage XC AGP 2x",
0x474F : "Rage XL PCI-66",
0x4750 : "1039",
0x4751 : "0x1002",
0x4752 : "Rage XL PCI",
0x4753 : "Rage XC PCI",
0x4754 : "Mach 64 VT",
0x4755 : "Rage 3D II+pci",
0x4756 : "Rage 3D IIC AGP",
0x4757 : "3D 11C AGP",
0x4758 : "210888GX",
0x4759 : "215r2qzua21",
0x475A : "215r2qua12",
0x4966 : "RV250",
0x4967 : "RV250",
0x496E : "RV250",
0x496F : "RV250",
0x4A48 : "R420",
0x4a49 : "R420",
0x4A4A : "R420",
0x4a4b : "R420",
0x4A4C : "R420",
0x4A4D : "R420GL",
0x4A4E : "M18",
0x4A4F : "R420",
0x4A50 : "R420",
0x4A54 : "R420",
0x4A68 : "R420",
0x4A69 : "R420",
0x4A6A : "R420",
0x4a6b : "R420",
0x4A6C : "R420",
0x4A6D : "R420GL",
0x4A6F : "R420",
0x4A70 : "R420",
0x4A74 : "R420",
0x4B49 : "R481",
0x4B4B : "R481",
0x4B4C : "R481",
0x4B69 : "R481",
0x4B6A : "R481",
0x4B6B : "R481",
0x4B6C : "R481",
0x4C42 : "B10E0E11",
0x4C44 : "Rage 3D LT Pro AGP",
0x4C45 : "",
0x4C46 : "Mobility M3 AGP",
0x4C47 : "ati rage pro",
0x4C49 : "123",
0x4C4D : "01541014",
0x4C4E : "216lo sasa25",
0x4C50 : "unknown",
0x4C51 : "113",
0x4C52 : "1241243",
0x4C53 : "216L0SASA25",
0x4C54 : "4372",
0x4C57 : "M7 [LW]",
0x4C58 : "",
0x4C59 : "Mobility 6",
0x4C5A : "",
0x4C64 : "",
0x4C66 : "RV250",
0x4C6E : "0x4C6E",
0x4D46 : "ATI mobility128",
0x4D4C : "216l0sasa25",
0x4D52 : "ATI Theater 550 Pro",
0x4D53 : "TVT2 Wonder Elite",
0x4E44 : "R300",
0x4E45 : "R300",
0x4e46 : "R300",
0x4E47 : "R300GL",
0x4E48 : "R350",
0x4E49 : "R350",
0x4E4A : "R360",
0x4E4B : "R350GL",
0x4E50 : "M10",
0x4E51 : "RV350",
0x4E52 : "M10",
0x4E54 : "M10GL",
0x4E56 : "M12",
0x4E64 : "R300",
0x4E65 : "R300",
0x4e66 : "R300",
0x4E67 : "R300GL",
0x4E68 : "R350",
0x4E69 : "R350",
0x4E6A : "R360",
0x4E6B : "R350GL",
0x4E71 : "RV350",
0x5041 : "gt",
0x5042 : "rage 128 pf pro agp ",
0x5043 : "1231324445",
0x5044 : "rv100",
0x5045 : "",
0x5046 : "R128",
0x5047 : "215R3BUA22",
0x5048 : "8212104D",
0x5049 : "R128",
0x504A : "Rage 128 Pro PJ PCI",
0x504B : "Rage 128 Pro PK AGP",
0x504C : "Rage 128 Pro PL AGP",
0x504D : "Rage 128 Pro PM PCI",
0x504E : "Rage 128 Pro PN AGP",
0x504F : "Rage 128 Pro PO AGP",
0x5050 : "Scheda Grafica Standard PCI(VGA)",
0x5051 : "Rage 128 Pro PQ AGP",
0x5052 : "Rage 128 Pro PR AGP",
0x5053 : "Rage 128 Pro PS PCI",
0x5054 : "Rage 128 Pro PT AGP",
0x5055 : "rage 128 pro agp 4x tmds",
0x5056 : "Rage 128 Pro PV PCI",
0x5057 : "Rage 128 Pro PW AGP",
0x5058 : "Rage 128 Pro",
0x5144 : "Radeon 7200 QD SDR/DDR",
0x5145 : "",
0x5146 : "",
0x5147 : "",
0x5148 : "R200",
0x5149 : "",
0x514A : "",
0x514B : "",
0x514C : "R200",
0x514D : "R200",
0x514E : "",
0x514F : "",
0x5157 : "RV200",
0x5158 : "radeon 9700 or 9200",
0x5159 : "RV100",
0x515A : "",
0x515E : "Radeon ES1000",
0x5168 : "ati",
0x5169 : "",
0x516A : "",
0x516B : "",
0x516C : "E7505",
0x516D : "R200",
0x5245 : "215R2QZUA21",
0x5246 : "Rage 128",
0x5247 : "Rage 32MB",
0x524B : "g01080-108",
0x524C : "",
0x5345 : "",
0x5346 : "Rage 128 SF 4x AGP 2x",
0x5347 : "",
0x5348 : "",
0x534B : "Rage 128 SK PCI",
0x534C : "Rage 128 SL AGP 2x",
0x534D : "Rage 128 SM AGP 4x",
0x534E : "Rage 128 4x",
0x5354 : "",
0x5446 : "unknown",
0x544C : "",
0x5452 : "",
0x5455 : "",
0x5457 : "RS200M",
0x5460 : "M22",
0x5461 : "M22",
0x5462 : "M24C",
0x5464 : "M22GL",
0x5548 : "R423",
0x5549 : "R423",
0x554A : "R423",
0x554b : "R423",
0x554D : "R430",
0x554E : "R430",
0x554F : "R430",
0x5550 : "R423GL",
0x5551 : "R423GL",
0x5568 : "R423",
0x5569 : "R423",
0x556A : "R423",
0x556B : "R423",
0x556D : "R430",
0x556E : "R430",
0x556F : "R430",
0x5570 : "R423GL",
0x5571 : "R423GL",
0x564A : "M26GL",
0x564B : "M26GL",
0x564F : "M26",
0x5652 : "M26",
0x5653 : "RV410",
0x5654 : "264VT",
0x5655 : "",
0x5656 : "Mach 64 VT4 PCI",
0x5657 : "RV410",
0x5673 : "M26",
0x5677 : "RV410",
0x5830 : "RS300",
0x5831 : "RS300",
0x5832 : "RS300",
0x5833 : "RS300M",
0x5834 : "RS300",
0x5835 : "RS300M",
0x5838 : "RS330M",
0x5854 : "RS480",
0x5874 : "RS482",
0x5940 : "RV280",
0x5941 : "RV280",
0x5950 : "RS480",
0x5954 : "RS482",
0x5955 : "RS480M",
0x5960 : "RV280",
0x5960 : "A051400005470",
0x5961 : "RV280",
0x5962 : "RV280",
0x5964 : "Radeon 9200",
0x5965 : "unknown",
0x5974 : "RS482",
0x5974 : "RS482",
0x5975 : "RS482M (200M)",
0x5a23 : "RD890",
0x5a31 : "RS400/133",
0x5A33 : "RC410",
0x5A41 : "0x5A41 ATI RADEON Xpress 1200 Series 0x1002",
0x5A41 : "RS400",
0x5A42 : "RS400M",
0x5A43 : "RS400",
0x5A60 : "SUBSYS_FF311179",
0x5A61 : "RC410",
0x5A61 : "RC410",
0x5A62 : "http://www.csd.toshiba.com/cgi-bin/tais/support/js",
0x5A63 : "RC410",
0x5b60 : "RV370",
0x5b62 : "RV380x",
0x5B63 : "REV_004&399D3C6A&0&0008",
0x5B64 : "RV370GL",
0x5B65 : "RV370",
0x5B60 : "RV370",
0x5B70 : "RV370",
0x5B72 : "RV380x",
0x5B73 : "RV370",
0x5B74 : "RV370GL",
0x5B75 : "RV370",
0x5C61 : "bk-ati ver008.016m.085.006",
0x5C63 : "RV280 (M9+)",
0x5D44 : "RV280",
0x5D45 : "RV280",
0x5D48 : "M28",
0x5D49 : "M28GL",
0x5d4a : "M28",
0x5d4d : "R480",
0x5d4f : "R480",
0x5D50 : "R480GL",
0x5d52 : "R480",
0x5D57 : "R423",
0x5d6d : "R480",
0x5D6F : "R480",
0x5D70 : "R480GL",
0x5D72 : "R480",
0x5D77 : "R423",
0x5E48 : "RV410GL",
0x5E4A : "RV410",
0x5E4B : "RV410",
0x5E4C : "RV410",
0x5E4D : "RV410",
0x5E4F : "RV410",
0x5E68 : "RV410GL",
0x5E6A : "RV410",
0x5E6B : "RV410",
0x5E6C : "RV410",
0x5E6D : "RV410",
0x5E6F : "RV410",
0x6076 : "123123132",
0x6718 : "CAYMAN XT",
0x6719 : "Cayman",
0x6738 : "HD6870",
0x6739 : "Barts (Pro)",
0x673E : "0x2310",
0x6740 : "Whistler",
0x6741 : "Whistler",
0x6741 : "AMD Radeon HD 7450M (6470M)、6630M、In",
0x6749 : "unknown",
0x674A : "V3900",
0x6750 : "1996",
0x6758 : "NI",
0x6759 : "1996",
0x6760 : "6470M",
0x6778 : "7470",
0x6779 : "AMD Radeon HD 6470m",
0x677B : "Unknown",
0x6840 : "SUBSYS",
0x6898 : "EG CYPRESS XT",
0x6899 : "EG CYPRESS PRO",
0x689C : "EG Cypress XT HEMLOCK",
0x68A0 : "EG BROADWAY XT",
0x68A1 : "EG BROADWAY PRO/LP",
0x68A8 : "AMD Radeon HD6870M (at least the one from Dell)",
0x68B0 : "EG BROADWAY XT",
0x68B8 : "EG JUNIPER XT",
0x68BA : "1482174B",
0x68BE : "EG JUNIPER LE",
0x68C1 : "DEV_68C1&SUBSYS_144A103C&REV_00",
0x68C8 : "RV830",
0x68c9 : "RV830",
0x68D8 : "Redwood",
0x68D9 : "RV830/Redwood",
0x68E0 : "HD 5470",
0x68E4 : "RV810",
0x68f9 : "Cedar",
0x700F : "A3/U1",
0x7010 : "RS200",
0x7100 : "R520",
0x7101 : "M58",
0x7102 : "M58",
0x7103 : "M58GL",
0x7104 : "R520GL",
0x7105 : "R520GL",
0x7106 : "M58GL",
0x7108 : "R520",
0x7109 : "R520",
0x710A : "R520",
0x710B : "R520",
0x710C : "R520",
0x710E : "R520GL",
0x710F : "R520GL",
0x7120 : "R520",
0x7124 : "R520GL",
0x7125 : "R520GL",
0x7128 : "R520",
0x7129 : "R520",
0x712A : "R520",
0x712B : "R520",
0x712C : "R520",
0x712E : "R520GL",
0x712F : "R520GL",
0x7140 : "RV515",
0x7142 : "RV515",
0x7143 : "RV505",
0x7145 : "M54",
0x7146 : "RV505",
0x7147 : "RV515",
0x7149 : "M52",
0x714A : "M52",
0x714B : "M52",
0x714C : "M52",
0x714D : "RV515",
0x714E : "RV515PCI",
0x7152 : "RV515GL",
0x7153 : "RV515GL",
0x715E : "RV515",
0x715F : "RV515",
0x7160 : "RV515",
0x7162 : "RV515",
0x7163 : "RV515",
0x7166 : "RV515",
0x7167 : "RV515",
0x716D : "RV515",
0x716E : "RV515PCI",
0x7172 : "RV515GL",
0x7173 : "RV515GL",
0x717E : "RV515",
0x717F : "RV515",
0x7180 : "RV515",
0x7181 : "RV515",
0x7183 : "RV515",
0x7186 : "M54",
0x7187 : "RV515",
0x7188 : "M64",
0x718A : "M54",
0x718B : "M52",
0x718C : "M52",
0x718D : "M54",
0x718F : "RV515PCI",
0x7193 : "RV515",
0x7196 : "M52",
0x719B : "RV515",
0x719F : "RV515",
0x71A0 : "RV515",
0x71A1 : "RV515",
0x71A3 : "RV515",
0x71A7 : "RV515",
0x71AF : "RV515PCI",
0x71B3 : "RV515",
0x71BB : "RV515",
0x71C0 : "RV530",
0x71C1 : "RV535",
0x71c2 : "RV530",
0x71C3 : "RV535",
0x71C4 : "M56GL",
0x71c5 : "M56",
0x71C6 : "RV530",
0x71C7 : "RV535",
0x71CD : "RV530",
0x71ce : "RV530",
0x71D2 : "RV530GL",
0x71D4 : "M56GL",
0x71D5 : "M56",
0x71D6 : "M56",
0x71DA : "RV530GL",
0x71DE : "M56",
0x71E0 : "RV530",
0x71E1 : "RV535",
0x71e2 : "RV530",
0x71E3 : "RV535",
0x71E6 : "RV530",
0x71E7 : "RV535",
0x71ED : "RV530",
0x71EE : "RV530",
0x71F2 : "RV530GL",
0x71FA : "RV530GL",
0x7205 : "1106",
0x7210 : "M71",
0x7211 : "M71",
0x7240 : "R580",
0x7243 : "R580",
0x7244 : "R580",
0x7245 : "R580",
0x7246 : "R580",
0x7247 : "R580",
0x7248 : "R580",
0x7249 : "R580",
0x724A : "R580",
0x724B : "R580",
0x724C : "R580",
0x724D : "R580",
0x724E : "R580",
0x724F : "R580",
0x7260 : "R580",
0x7263 : "R580",
0x7264 : "R580",
0x7265 : "R580",
0x7266 : "R580",
0x7267 : "R580",
0x7268 : "R580",
0x7269 : "R580",
0x726A : "R580",
0x726B : "R580",
0x726C : "R580",
0x726D : "R580",
0x726E : "R580",
0x726F : "R580",
0x7280 : "R580",
0x7284 : "M58",
0x7286 : "R580",
0x7288 : "R580",
0x7291 : "R560",
0x7293 : "R580",
0x72A0 : "R580",
0x72A8 : "R580",
0x72B1 : "R580",
0x72B3 : "R580",
0x7833 : "RS350",
0x79 : "unknown",
0x791 : "RS690M",
0x791a : "791A",
0x791E : "RS690",
0x791F : "RS690M",
0x7912 : "SUBSYS_826D1043",
0x7937 : "Samsung R25P",
0x793F : "RS600",
0x7941 : "RS690M",
0x7942 : "RS600M",
0x796E : "RS690",
0x8086 : "1050",
0x9000 : "RV350",
0x9094 : "RV730",
0x9400 : "R600",
0x9401 : "R600",
0x9402 : "R600",
0x9403 : "R600",
0x9405 : "R600",
0x940A : "R600GL",
0x940B : "R600GL",
0x940F : "R600GL",
0x9440 : "RV770",
0x9441 : "R700",
0x9442 : "RV770",
0x9443 : "R700",
0x9444 : "RV770",
0x9446 : "RV770",
0x9447 : "R700",
0x944A : "M98",
0x944B : "M98",
0x944C : "RV770",
0x944E : "RV770",
0x9450 : "RV770",
0x9452 : "RV770",
0x9456 : "RV770",
0x945A : "M98",
0x9460 : "RV790",
0x9462 : "RV790",
0x9480 : "M96",
0x9487 : "RV730",
0x9488 : "M96",
0x948F : "RV730",
0x9490 : "RV730",
0x9491 : "M96",
0x9495 : "RV730",
0x9498 : "RV730",
0x949C : "RV730",
0x949E : "RV730",
0x949F : "RV730",
0x94A0 : "M97",
0x94A1 : "M97",
0x94A3 : "M97",
0x94B1 : "RV740",
0x94B3 : "RV740",
0x94B4 : "RV740",
0x94B5 : "AA38",
0x94C1 : "RV610-DT (Pro)",
0x94C3 : "RV610-DT (LE)",
0x94C4 : "RV610LE",
0x94C5 : "RV610",
0x94C7 : "RV610",
0x94C8 : "M72",
0x94C9 : "M72",
0x94CB : "M72",
0x94CC : "RV610",
0x9501 : "RV670 XT",
0x9504 : "M76",
0x9505 : "RV630",
0x9506 : "M76",
0x9507 : "RV670",
0x9508 : "M76",
0x9509 : "M76",
0x950F : "R680",
0x9511 : "RV630GL",
0x9513 : "R680",
0x9515 : "RV670 AGP",
0x9519 : "RV670",
0x9540 : "RV710",
0x9541 : "RV710",
0x954E : "RV710",
0x954F : "RV710",
0x9552 : "M92",
0x9553 : "M92",
0x9555 : "M93",
0x9557 : "M93",
0x9581 : "M76M",
0x9583 : "M76",
0x9586 : "RV630",
0x9587 : "RV630 PRO",
0x9588 : "RV630 XT",
0x9589 : "ПРО RV630",
0x958B : "M76",
0x958C : "RV630GL",
0x958D : "RV630GL",
0x958E : "RV630",
0x958F : "M76",
0x9590 : "RV630",
0x9591 : "M86-M",
0x9593 : "M86",
0x9595 : "M86",
0x9596 : "RV630",
0x9597 : "RV630",
0x9598 : "RV630",
0x9599 : "RV630",
0x959B : "M86",
0x95C0 : "RV610",
0x95C2 : "M72",
0x95c4 : "M82-S",
0x95C5 : "RV620 LE",
0x95C6 : "RV620",
0x95C7 : "RV610",
0x95C9 : "RV620",
0x95CC : "RV620",
0x95CD : "RV610",
0x95CE : "RV610",
0x95CF : "RV610",
0x9610 : "RS780",
0x9611 : "RS780",
0x9612 : "RS780M",
0x9613 : "RS780M",
0x9614 : "RS780",
0x9615 : "RS780",
0x9616 : "RS780",
0x9644 : "A4-3400",
0x9647 : "AMD A6-3420M APU With AMD Radeon HD 6520G",
0x9648 : " 9648",
0x9649 : "HD 6480G",
0x9710 : "RS880",
0x9711 : "RS880",
0x9712 : "4250",
0x9713 : "RS880MC",
0x9715 : "RS880",
0x9802 : "AMD E-350",
0x9803 : "2411E6FE",
0x9804 : "AMD Radeon HD 6310 Graphics AMD Radeon HD 6310 Gr",
0x9806 : "AMD Radeon HD 6320",
0x9807 : "unknow",
0x9808 : "E2-1800",
0x9809 : "7310M",
0x9876 : "ATI GTC (GT-C2U2)",
0x9999 : "(0x9498",
0xAA01 : "Ati Function driver for high definition audio1",
0xAA08 : "All with HDMI support",
0xAA10 : "677",
0xAA20 : "RV630",
0xAA28 : "3400",
0xaa68 : " 0x040300",
0xAC12 : "Theater HD T507",
0xCAB0 : "A3/U1",
0xCAB1 : "A3/U1",
0xcab2 : "RS200",
0xCBB2 : "RS200",
0x0876 : "",
7800 : "",
},
0x1003 : { 0x0201 : "GUI Accelerator",
},
0x1004 : { 0x0005 : "DEV_0200",
0x0006 : "ISA Bridge",
0x0007 : "Wildcat System Controller",
0x0008 : "Wildcat ISA Bridge",
0x0009 : "",
0x000C : "",
0x000D : "",
0x0100 : "CPU to PCI Bridge for notebook",
0x0101 : "Peripheral Controller",
0x0102 : "PCI to PCI Bridge",
0x0103 : "PCI to ISA Bridge",
0x0104 : "Host Bridge",
0x0105 : "IrDA Controller",
0x0200 : "RISC GUI Accelerator",
0x0280 : "RISC GUI Accelerator",
0x0304 : "ThunderBird PCI Audio Accelerator",
0x0305 : "ThunderBird joystick port",
0x0306 : "ThunderBird 16650 UART",
0x0307 : "Philips Seismic Edge 705",
0x0308 : "Philips PSC705 GamePort Enumerator",
0x0702 : "Golden Gate II",
},
0x1006 : { 0x3044 : "OHCI Compliant IEEE 1394 Host Controller",
},
0x1008 : { 0x9876 : "23",
},
0x100A : { 0x8235 : "U87088R06",
},
0x100B : { 0x0001 : "10/100 Ethernet MAC",
0x0002 : "PCI-IDE DMA Master Mode Interface Ctrlr",
0x000E : "Legacy I/O Controller",
0x000F : "IEEE 1394 OHCI Controller",
0x0011 : "PCI System I/O",
0x0012 : "USB Controller",
0x001B : "Advanced PCI Audio Accelerator",
0x0020 : "MacPhyter 10/100 Mb/s Ethernet MAC & PHY",
0x0020 : "10/100 MacPhyter3v PCI Adapter",
0x0021 : "PCI to ISA Bridge",
0x0022 : "10/100/1000 Mb/s PCI Ethernet NIC",
0x0028 : "PCI Host Bridge",
0x002A : "GeodeLink PCI South Bridge",
0x002D : "Geode IDE Controller",
0x002E : "GEODE - GX3 Audio CS5535",
0x002F : "USB Controller",
0x0030 : "Geode VGA Compatible Device",
0x0500 : "LPC Bridge and GPIO",
0x0501 : "SMI Status and ACPI",
0x0502 : "IDE Controller",
0x0503 : "XpressAUDIO",
0x0504 : "Video Processor",
0x0505 : "X-Bus Expansion Interface",
0x0510 : "LPC Bridge and GPIO",
0x0511 : "SMI Status and ACPI",
0x0515 : "X-Bus Expansion Interface",
0x23 : "",
0xD001 : "PCI-IDE Interface",
},
0x100C : { 0x3202 : "GUI Accelerator",
0x3205 : "GUI Accelerator",
0x3206 : "GUI Accelerator",
0x3207 : "GUI Accelerator",
0x3208 : "Graphics/Multimedia Engine",
0x4702 : "",
},
0x100E : { 0x0564 : "Host Bridge",
0x55CC : "South Bridge",
0x9000 : "WeitekPower GUI Accelerator",
0x9001 : "GUI Accelerator",
0x9100 : "GUI Accelerator",
},
0x1011 : { 0x0001 : "PCI-PCI Bridge",
0x0002 : "Tulip Ethernet Adapter",
0x0004 : "PCI Graphics Accelerator",
0x0007 : "NV-RAM",
0x0008 : "SCSI to SCSI Adapter",
0x0009 : "Fast Ethernet Ctrlr",
0x000A : "Video Codec",
0x000C : "6IfPpL <a href=",
0x000D : "TGA2 PDXGB",
0x000F : "FDDI",
0x0014 : "Tulip Plus Ethernet Adapter",
0x0016 : "ATM",
0x0019 : "PCI/CardBus 10/100 Mbit Ethernet Ctlr",
0x0021 : "PCI-PCI Bridge",
0x0022 : "PCI-PCI Bridge",
0x0023 : "PCI to PCI Bridge",
0x0024 : "PCI-PCI Bridge",
0x0025 : "PCI-PCI Bridge",
0x0026 : "PCI-PCI Bridge",
0x0034 : "CardBus",
0x0045 : "PCI to PCI Bridge",
0x0046 : "PCI-to-PCI Bridge",
0x1011 : "PCI-PCI Bridge",
0x1065 : "Mylex DAC1164P Disk Array Controller",
0x2000 : "Fault Mgr (3.3v/5v Universal PCI)",
},
0x1013 : { 0x0038 : "pci",
0x0040 : "Flat Panel GUI Accelerator",
0x004C : "64-bit Accelerated LCD/CRT Controller",
0x00A0 : "GUI Accelerator",
0x00A2 : "Alpine GUI Accelerator",
0x00A4 : "Alpine GUI Accelerator",
0x00A8 : "Alpine GUI Accelerator",
0x00AC : "Video card (i guess?)",
0x00B8 : "64-bit VisualMedia Accelerator",
0x00BC : "64-bit SGRAM GUI accelerator",
0x00D0 : "Laguna VisualMedia graphics accelerator",
0x00D4 : "Laguna 3D VisualMedia Graphics Accel",
0x00D5 : "Laguna BD",
0x00D6 : "Laguna 3D VisualMedia Graphics Accel",
0x00E8 : "",
0x1013 : "accelerator do audio do pci de sound fusion",
0x1100 : "PCI-to-PC Card host adapter",
0x1110 : "PCMCIA/CardBus Controller",
0x1112 : "PCMCIA/CardBus Controller",
0x1113 : "PCI-to-CardBus Host Adapter",
0x1200 : "Nordic GUI Accelerator",
0x1202 : "Viking GUI Accelerator",
0x1204 : "Nordic-lite VGA Cntrlr",
0x4000 : "Ambient CLM Data Fax Voice",
0x4400 : "Communications Controller",
0x6001 : "CrystalClear SoundFusion PCI Audio Accelerator",
0x6003 : "Crystal Sound Fusion a",
0x6004 : "CrystalClear SoundFusion PCI Audio Accel",
0x6005 : "Crystal Soundfusion(tm) CS 4206 WDM Audio",
0x9876 : "SoundFusion PCI Audio Accelerator",
},
0x1014 : { 0x0002 : "MCA Bridge",
0x0005 : "CPU Bridge",
0x0007 : "CPU Bridge",
0x000A : "ISA Bridge w/PnP",
0x0017 : "CPU to PCI Bridge",
0x0018 : "TR Auto LANStreamer",
0x001B : "Graphics Adapter",
0x001D : "scsi-2 fast pci adapter",
0x0020 : "MCA Bridge",
0x0022 : "PCI to PCI Bridge ",
0x002D : "",
0x002E : "Coppertime RAID SCSI Adapter",
0x0036 : "32-bit LocalBus Bridge",
0x0037 : "PowerPC to PCI Bridge and Memory Ctrlr",
0x003A : "CPU to PCI Bridge",
0x003E : "IBM Token Ring PCI",
0x0045 : "SSA Adapter",
0x0046 : "Interrupt Controller",
0x0047 : "PCI to PCI Bridge",
0x0048 : "PCI to PCI Bridge",
0x0049 : "Warhead SCSI Controller",
0x004D : "MPEG-2 Decoder",
0x004E : "ATM Controller",
0x004F : "ATM Controller",
0x0050 : "ATM Controller",
0x0053 : "25 MBit ATM controller",
0x0057 : "MPEG PCI Bridge",
0x005C : "10/100 PCI Ethernet Adapter",
0x005D : "TCP/IP networking device",
0x007C : "ATM Controller",
0x007D : "MPEG-2 Decoder",
0x0090 : "",
0x0095 : "PCI Docking Bridge",
0x0096 : "Chukar chipset SCSI Controller",
0x00A1 : "ATM support device",
0x00A5 : "ATM Controller",
0x00A6 : "ATM 155Mbps MM Controller",
0x00B7 : "256-bit Graphics Rasterizer",
0x00BE : "ATM 622Mbps Controller",
0x00CE : "Adapter 2 Token Ring Card",
0x00F9 : "Memory Controller and PCI Bridge",
0x00FC : "PCI-64 Bridge",
0x0105 : "PCI-32 Bridge",
0x010F : "Remote Supervisor+Serial Port+Mouse/Keyb",
0x011B : "Raid controller",
0x0142 : "Video Compositor Input",
0x0144 : "Video Compositor Output",
0x0153 : "",
0x0156 : "PLB to PCI Bridge",
0x0170 : "Rasterizer/IBM GT1000 Geometr",
0x0188 : "PCI Bridge",
0x01a2 : "Modem: Intel Corporation 82440MX AC'97 Modem Controller (prog-if 00 [Generic])",
0x01A7 : "PCI-X Bridge R1.1",
0x01BD : "Morpheus SCSI RAID Controller",
0x01ef : "PLB to PCI-X Bridge",
0x0246 : "",
0x027F : "Embedded PowerPC CPU",
0x0289 : "0890",
0x028c : "SCSI Storage Controller",
0x0295 : "IBM SurePOS Riser Card Function 0",
0x0297 : "IBM SurePOS Riser Card Function 1 (UARTs)",
0x02A1 : "Calgary PCI-X Host Bridge",
0x0302 : "PCI-X Host Bridge",
0x0308 : "IBM CalIOC2 (Calgary on PCI-E)",
0xFFFF : "Interrupt Controller",
0x37C0 : "IBM Netfinity Advanced System Management Processor",
0x37D0 : "n/a",
},
0x1017 : { 0x5343 : "SPEA 3D Accelerator",
},
0x1018 : { 0x3330 : "5444469821",
},
0x1019 : { 0x1B10 : "VIA chipset",
0x9876 : "Intel(R) Celeron(R) CPU 2.80GHz",
},
0x101A : { 0x0005 : "100VG/AnyLAN Adapter",
0x0009 : "PCI-X dual port ",
},
0x101E : { 0x9010 : "Ultra Wide SCSI RAID Controller2",
0x9030 : "EIDE Controller",
0x9031 : "EIDE Controller",
0x9032 : "IDE and SCSI Cntrlr",
0x9033 : "SCSI Controller",
0x9040 : "Multimedia card",
0x9060 : "Ultra GT RAID Controller",
0x9063 : "Remote Assistant",
0x9095 : "SGPIO/SES/IPMI Initiator",
},
0x1022 : { 0x1100 : "HyperTransport Technology Configuration",
0x1101 : "Address Map",
0x1102 : "AMD Hammer - DRAM Controller ",
0x1103 : "AMD Hammer - Miscellaneous Control ",
0x2000 : "PCnet LANCE PCI Ethernet Controller",
0x2001 : "PCnet-Home Networking Ctrlr (1/10 Mbps)",
0x2003 : "Wireless LAN chipset SMC 2602W V3 http://www.smc.com/index.cfm?event=downloads.doSearchCriteria&loca",
0x2020 : "SCSI Controller",
0x2040 : "Ethernet Controller",
0x2081 : "GeodeLX graphics adapter",
0x2082 : "Geode GX3 AES Crypto Driver",
0x208F : "GeodeLink PCI South Bridge",
0x2093 : "CS5536 Audio Controller",
0x2094 : "CS5536 OHCI USB Host Controller",
0x2095 : "CS5536 EHCI USB Host Controller",
0x2096 : "CS5536 USB Device Controller",
0x2097 : "CS5536 USB OTG Controller",
0x209A : "CS5536 IDE Controller",
0x2433 : "Chill Control Connector",
0x3000 : "ELAN Microcontroller PCI Host Bridge",
0x5e4b : "Radeon X700 Pro",
0x7004 : "CPU to PCI Bridge",
0x7006 : "Processor-to-PCI Bridge / Memory Ctrlr",
0x7007 : "AGP and PCI-to-PCI Bridge (1x/2x AGP)",
0x700A : "AGP Host to PCI Bridge",
0x700B : "AGP PCI to PCI Bridge",
0x700C : "CPU to PCI Bridge (SMP chipset)",
0x700D : "CPU to PCI Bridge (AGP 4x)",
0x700E : "North Bridge",
0x700F : "CPU to AGP Bridge (AGP 4x)",
0x7400 : "PCI to ISA Bridge",
0x7401 : "Bus Master IDE Controller",
0x7403 : "Power Management Controller",
0x7404 : "PCI to USB Open Host Controller",
0x7408 : "PCI-ISA Bridge",
0x7409 : "EIDE Controller",
0x740B : "Power Management",
0x740C : "USB Open Host Controller",
0x7410 : "PCI to ISA/LPC Bridge",
0x7411 : "Enhanced IDE Controller",
0x7412 : "USB Controller",
0x7413 : "Power Management Controller",
0x7414 : "USB OpenHCI Host Controller",
0x7440 : "LPC Bridge",
0x7441 : "EIDE Controller",
0x7443 : "System Management",
0x7445 : "AC97 Audio",
0x7446 : "AC97 Modem",
0x7448 : "PCI Bridge",
0x7449 : "USB Controller",
0x7450 : "PCI-X Bridge",
0x7451 : "PCI-X IOAPIC",
0x7454 : "System Controller",
0x7455 : "AGP Bridge",
0x7458 : "PCI-X Bridge",
0x7459 : "PCI-X IOAPIC",
0x7460 : "PCI Bridge",
0x7461 : "USB 2.0 Controller",
0x7462 : "Ethernet Controller",
0x7463 : "USB Enhanced Host Controller",
0x7464 : "USB OpenHCI Host Controller",
0x7468 : "LPC Bridge",
0x7469 : "UltraATA/133 Controller",
0x746A : "SMBus 2.0 Controller",
0x746B : "System Management",
0x746D : " Audio Controller",
0x746E : "AC'97 Modem",
0x756B : "ACPI Controller",
0x7801 : "AMD SATA Controller",
0x7801 : "AMD SATA Controller",
0x780b : "SM Bus controller",
0x7812 : "AMD USB 3.0 Host Controller",
0x840 : "Used to blow up the motherboard. Highly explosive. Use at ur own risk",
0x9642 : "AMD Radeon HD6370D",
},
0x1023 : { 0x0194 : "CardBus Controller",
0x2000 : "advanced PCI DirectSound accelerator",
0x2001 : "PCI Audio",
0x2100 : "Video Accelerator",
0x2200 : "Video adapter",
0x8400 : "sausgauos",
0x8420 : "Trident Cyber Blade i7 AGP (55)",
0x8500 : "Via Tech VT8361/VT8601 Graphics Controller",
0x8520 : "Windows xp",
0x8620 : "trident",
0x8820 : "TRIDENT DISPLAY CONTROLER /CyberALADDiN-T Driver",
0x9320 : "32-bit GUI Accelerator",
0x9350 : "32-bit GUI Accelerator",
0x9360 : "Flat panel Cntrlr",
0x9382 : "",
0x9383 : "",
0x9385 : "",
0x9386 : "Video Accelerator",
0x9388 : "Video Accelerator",
0x9397 : "Video Accelerator 3D",
0x939A : "Video Accelerator",
0x9420 : "DGi GUI Accelerator",
0x9430 : "GUI Accelerator",
0x9440 : "DGi GUI Acclerator",
0x9460 : "32-bit GUI Accelerator",
0x9470 : "",
0x9520 : "Video Accelerator",
0x9525 : "Video Accelerator",
0x9540 : "Video Acclerator",
0x9660 : "GUI Accelerator",
0x9680 : "GUI Accelerator",
0x9682 : "Trident A CAB01",
0x9683 : "GUI Accelerator",
0x9685 : "2MB VGA",
0x9750 : "trident dgi",
0x9753 : "Video Accelerator",
0x9754 : "Wave Video Accelerator",
0x9759 : "Image GUI Accelerator",
0x9783 : "",
0x9785 : "",
0x9850 : "4mb",
0x9880 : "gggggg",
0x9910 : "CyberBlade XP",
0x9930 : "",
0x9960 : "Trident Video Accelerator CyberBlade-1A31",
},
0x1025 : { 0x0028 : "Agere Systems soft modem chip",
0x1435 : "USBVID_0502&PID_3476&MI_016&207B7CA8&0&0001",
0x1445 : "VL Bridge & EIDE",
0x1449 : "ISA Bridge",
0x1451 : "Pentium Chipset",
0x1461 : "P54C Chipset",
0x1489 : "",
0x1511 : "",
0x1512 : "",
0x1513 : "",
0x1521 : "CPU Bridge",
0x1523 : "ISA Bridge",
0x1531 : "North Bridge",
0x1533 : "ISA South Bridge",
0x1535 : "PCI South Bridge",
0x1541 : "AGP PCI North Bridge Aladdin V/V+",
0x1542 : "AGP+PCI North Bridge",
0x1543 : "PCi South Bridge Aladdin IV+/V",
0x1561 : "driver video",
0x1621 : "PCI North Bridge Aladdin Pro II",
0x1631 : "PCI North Bridge Aladdin Pro III",
0x1641 : "PCI North Bridge Aladdin Pro IV",
0x3141 : "GUI Accelerator",
0x3143 : "GUI Accelerator",
0x3145 : "GUI Accelerator",
0x3147 : "GUI Accelerator",
0x3149 : "GUI Accelerator",
0x3151 : "GUI Accelerator",
0x3307 : "MPEG-1 Decoder",
0x3309 : "MPEG Decoder",
0x5212 : "",
0x5215 : "EIDE Controller",
0x5217 : "I/O Controller",
0x5219 : "I/O Controller",
0x5225 : "EIDE Controller",
0x5229 : "EIDE Controlle",
0x5235 : "I/O Controller",
0x5237 : "Intel(R) 5 Series/3400 Series Chipset Family 4 Port SATA AHCI Controller - 3B29",
0x5239 : "",
0x5240 : "EIDE Controller",
0x5241 : "PCMCIA Bridge",
0x5242 : "General Purpose Controller",
0x5243 : "PCI to PCI Bridge",
0x5244 : "Floppy Disk Controller",
0x5247 : "PCI-PCI Bridge",
0x5427 : "PCI to AGP Bridge",
0x5451 : "PCI AC-Link Controller Audio Device",
0x5453 : "M5453 AC-Link Controller Modem Device",
0x7101 : "PCI PMU Power Management Controller",
},
0x1028 : { 0x0001 : "Expandable RAID Controller (PERC) (SCSI)",
0x0002 : "Expandable RAID Controller",
0x0003 : "Expandable RAID Controller",
0x0004 : "Expandable RAID Controller",
0x0005 : "Expandable RAID Controller",
0x0006 : "Expandable RAID Controller",
0x0007 : "Remote Assistant Card",
0x0008 : "RAC Virtual UART Port",
0x000A : "Expandable RAID Controller",
0x000C : "Embedded Systems Management Device 4",
0x000D : "LSI53C895 PCI to Ultra2 SCSI I/O Processor with LVD Link",
0x000E : "PERC 4/DI Raid Controller",
0x0010 : "HJ866 - ESM4 Remote .Access card DRAC4",
0x0011 : "Dell Remote Access Controller v4",
0x0012 : "Dell RAC v4 Virtual UART",
0x0013 : "Expandable RAID Controller",
0x0014 : "Dell Remote Access Controller subsystem",
0x0015 : "Integrated RAID controller",
0x012c : "Intel Gigabit controller",
0x016d : "Dell PRO/1000 MT Network Connection",
0x0287 : "Adaptec 2200S SCSI RAID controller",
0x1000 : "A Intel 537 epg v.92 modem repackaged by dell",
0x1050 : "ethernet controller",
0x1f0c : "Dell PERC 6/i Integrated RAID Controller",
0x3002 : "Dell Wireless 1702 Bluetooth v3.0+HS",
0x3582 : "video controller",
0x9876 : "Expandable RAID Controller",
},
0x102A : { 0x0000 : "4 port usb hub",
0x0003 : "USBVID_0000&PID_00005&18BB29D0&1&2",
0x0010 : "i486 Chipset",
0x002A : "4 port usb hub",
0x102A : "P5 Chipset",
0x9876 : "P5 CHIPSET",
},
0x102B : { 0x0010 : "Impression?",
0x0040 : "Matrox P650 very new model (20080724)",
0x051 : "matrox",
0x0518 : "Atlas GUI Accelerator",
0x0519 : "Strorm GUI Accelerator",
0x051A : "Hurricane/Cyclone 64-bit graphics chip",
0x051B : "Matrox",
0x051E : "Chinook",
0x051F : "Mistral",
0x0520 : "AGP",
0x0521 : "102B",
0x0522 : "Matrox G200e (ServerEngines) - English",
0x0525 : "Intel Pentium III",
0x0527 : "",
0x0528 : "Parhelia 128MB/256MB/PCI/HR256",
0x0530 : "Matrox G200eV",
0x0534 : "G200eR",
0x0540 : "M9138 LP PCIe x16",
0x0D10 : "Athena GUI accelerator",
0x1000 : "Twister",
0x1001 : "Twister AGP",
0x1525 : "",
0x1527 : "",
0x2007 : "GUI+3D Accelerator",
0x2527 : "AGP Chipset",
0x2537 : "Parhelia Chipset AGP",
0x2538 : "Matrox Millennium P650 LP PCIe 64",
0x2539 : "Matrox Graphics Board dual DVI",
0x4536 : "Video Capture Card",
0x522 : "Matrox G200e (ServerEngines)",
0x525 : "G45+",
0x532 : "Matrox G200eW 8 MB DDR2 ",
0x6573 : "10/100 Multiport Switch NIC",
0x80A0 : "Multimedia Device",
0x9876 : "Multimedia device",
},
0x102C : { 0x00B8 : "Wingine DGX - DRAM Graphics Accelerator",
0x00C0 : "AGP/PCI Flat Panel/CRT VGA Accelerator",
0x00D0 : "Flat panel/crt VGA Cntrlr",
0x00D8 : "Flat Panel/CRT VGA Controller",
0x00DC : "GUI Accelerator",
0x00E0 : "LCD/CRT controller",
0x00E4 : "Flat Panel/LCD CRT GUI Accelerator",
0x00E5 : "VGA GUI Accelerator",
0x00F0 : "vga Controller",
0x00F4 : "graphic driver",
0x00F5 : "GUI Controller",
0x01E0 : "PCI Flat Panel/CRT VGA Accelerator",
0x0C30 : "AGP/PCI Flat Panel/CRT VGA Accelerator",
},
0x102D : { 0x50DC : "Audio",
},
0x102F : { 0x0009 : "CPU Bridge",
0x000A : "CPU Bridge?",
0x0020 : "ATM PCI Adapter",
0x0030 : "8086",
0x0031 : "Integrated 10/100 Mbit Ethernet Controller",
0x0100 : "Realtek RTS5208 Card Reader",
0x0105 : "GOKU-S Bus Master IDE Controller",
0x0106 : "GOKU-S USB Host Controller",
0x0107 : "GOKU-S USB Device Controller",
0x0108 : "GOKU-S I2C Bus/SIO/GPIO Controller",
0x0180 : "MIPS Processor",
0x0181 : "MIPS RISC PCI Controller (PCIC)",
0x0182 : "MIPS RISC PCI Controller (PCIC)",
0x01BA : "SpursEngine",
0x0805 : "1179",
0x102F : "1179",
},
0x1031 : { 0x5601 : "I/O & JPEG",
0x5607 : "video in and out with motion jpeg compression and deco",
0x5631 : "",
0x6057 : "DC30D-601601-4.0",
},
0x1033 : { 0x0001 : "PCI to 486 like bus Bridge",
0x0002 : "PCI to VL98 Bridge",
0x0003 : "ATM Controller",
0x0004 : "PCI bus Bridge",
0x0005 : "PCI to 486 like peripheral bus Bridge",
0x0006 : "GUI Accelerator",
0x0007 : "PCI to ux-bus Bridge",
0x0008 : "GUI Accelerator (vga equivalent)",
0x0009 : "graphic Cntrlr for 98",
0x001A : "",
0x001D : "NEASCOT-S20 ATM Integrated SAR Ctrlr",
0x0021 : "Nile I",
0x0029 : "3D Accelerator",
0x002A : "3D Accelerator",
0x002f : "1394 Host Controller",
0x0034 : "0x0034",
0x0035 : "Dual OHCI controllers plus Single EHCI controller",
0x0036 : "NEASCOT-S40C ATM Light SAR Controller",
0x003E : "NAPCCARD CardBus Controller",
0x0046 : "3D Accelerator",
0x005A : "Nile 4",
0x0063 : "Firewarden IEEE1394 OHCI Host Controller",
0x0067 : "PowerVR series II graphics processor",
0x0074 : "56k Voice Modem",
0x009B : "",
0x00A6 : "",
0x00BE : "64-bit CPU with Northbridge",
0x00CD : "IEEE1394 1-Chip OHCI Host Controller",
0x00CE : "IEEE1394 1-Chip OHCI Host Controller",
0x00E0 : "USB 2.0 Host Controller",
0x00E0 : "USB 2.0 Host Controller",
0x00E7 : "IEEE1394 OHCI 1.1 3-port PHY-Link Ctrlr",
0x00F2 : "IEEE1394+OHCI+1.1+3-port+PHY-Link+Ctrlr",
0x0165 : "AVerMedia A313 MiniCard Hybrid DVB-T",
0x0194 : "Renesas Electronics USB 3.0 Host Controller",
0x0520 : "1394 CARD",
0x1033 : "NEC PCI to USB Open Host Controller",
0x9876 : "USB 2.0 Host Controller",
},
0x1036 : { 0x0000 : "Fast SCSI",
},
0x1039 : { 6529 : "",
0 : "",
0x7012 : "PCI Audio Accelerator",
0x0001 : "Anthlon 64 cpu to PCI bridge",
0x0002 : "Virtual PCI to PCI Bridge (AGP)",
0x0003 : "SiS AGP Controller / SiS Accelerated Graphics Port ",
0x0005 : "Pentium chipset",
0x0006 : "PCI/ISA Cache Memory Controller (PCMC)",
0x0008 : "PCI System I/O (PSIO)",
0x0009 : "SIS PMU device",
0x0016 : "SMBus ControllerP4kjc",
0x0018 : "vga",
0x0160 : "SiS160 811 Wireless LAN Adapter",
0x0180 : "SiS 180/181 RAID Controller ",
0x0181 : "Raid Controller(?Mode Raid1)",
0x0182 : "Raid Controller(?Mode Raid0+1)",
0x0183 : "?SATA",
0x0186 : "0330",
0x0190 : " SiS965",
0x0191 : "SIS191",
0x0200 : "Onboard Graphics Controller",
0x0204 : "PCI1",
0x0205 : "PCI Graphics & Video Accelerator",
0x0300 : "GUI Accelerator+3D",
0x0305 : "2D/3D/Video/DVD Accelerator",
0x0315 : "2D/3D Accelerator",
0x0325 : "Silicon Integrated Systems (SiS)",
0x0330 : "Xabre 2D/3D Accelerator (AG400T8-D64)",
0x0406 : "PCI/ISA Cache Memory Controller (PCMC)",
0x0496 : "CPU to PCI & PCI to ISA Bridge",
0x0530 : "Host-to-PCI bridge",
0x0540 : "Host-to-PCI Bridge",
0x0550 : "North Bridge",
0x0596 : "Pentium PCI chipset with IDE",
0x0597 : "EIDE Controller (step C)",
0x0601 : "PCI EIDE Controller",
0x0620 : "Host-to-PCI Bridge",
0x0630 : "Host-to-PCI Bridge",
0x0635 : "Host-to-PCI Bridge",
0x0640 : "Host-to-PCI Bridge",
0x0645 : "Host-to-PCI Bridge",
0x0646 : "Host-to-PCI Bridge",
0x0648 : "Host-to-PCI Bridge",
0x0649 : "Host-to-PCI Bridge",
0x0650 : "Host-to-PCI Bridge",
0x0651 : "Host-to-PCI Bridge",
0x0655 : "Host-to-PCI Bridge",
0x0656 : "CPU to PCI Bridge",
0x0658 : "CPU to PCI Bridge",
0x0659 : "CPU to PCI Bridge",
0x0660 : "Host-to-PCI Bridge",
0x0661 : "SiS 661FX/GX Chipset - Host-PCI Bridge",
0x0662 : "CPU to PCI Bridge",
0x0663 : "CPU to PCI Bridge",
0x0730 : "Host-to-PCI Bridge",
0x0735 : "Host-to-PCI Bridge",
0x0740 : "LPC Bridge",
0x0741 : "CPU to PCI Bridge",
0x0745 : "Host-to-PCI Bridge",
0x0746 : "Host-to-PCI Bridge",
0x0748 : "CPU to PCI Bridge",
0x0755 : "Host-to-PCI Bridge",
0x0756 : "CPU to PCI Bridge",
0x0760 : "Athlon 64 CPU to PCI Bridge",
0x0761 : "Athlon 64 CPU to PCI Bridge",
0x0762 : "Athlon 64 CPU to PCI Bridge",
0x0900 : "SiS 900 Fast Ethernet Adapter",
0x0901 : "SiS900 10/100 Ethernet Adapter",
0x0962 : "LPC Bridge",
0x0963 : "PCI to ISA Bridge",
0x0964 : "SiS 964 MuTIOL Media I/O Bridge ",
0x0999 : "1039",
0x1039 : "SiS5597 SVGAa",
0x1040 : "",
0x10ec : "bus controler",
0x1182 : "Raid Controller(?Mode Raid5)",
0x1183 : "SATA IDE Controller",
0x1184 : "Raid/AHCI Controller",
0x1185 : "AHCI Controller",
0x1234 : "SiS5597 SVGAa",
0x191 : "PCI /ven_1039",
0x3602 : "IDE Controller",
0x4321 : "Video Controller (VGA Compatible)",
0x5107 : "Hot Docking Controller",
0x5300 : "AGP",
0x5315 : "GUI Accelerator",
0x5401 : "486 PCI Chipset",
0x5511 : "PCI/ISA System Memory Controller",
0x5513 : "SiS 5513 IDE UDMA Controller / SiS 85C513 IDE Controller",
0x5517 : "CPU to PCI Bridge",
0x5518 : "UDMA IDE Controller",
0x5571 : "Memory/PCI bridge",
0x5581 : "p5 chipset",
0x5582 : "PCI to ISA Bridge",
0x5591 : "1969",
0x5596 : " VGA Controller",
0x5597 : "Host to PCI bridge",
0x5600 : "Host-to-PCI Bridge",
0x5630 : "Host-to-PCI Bridge",
0x5811 : "",
0x6204 : "video decoder/mpeg interface",
0x6205 : "PCI VGA Controller",
0x6225 : "PCI Graphics & Video Accelerator",
0x6236 : "Graphics",
0x6300 : "GUI Accelerator+3D",
0x6306 : "Integrated 3D SVGA Controller",
0x6325 : "sis-651dx",
0x6326 : "sis 6326 AGP",
0x6330 : "GUI 2D/3D Accelerator",
0x6331 : "USB Host Controller",
0x6351 : "SiS IGP Graphics family SIS66x/SIS76x & SIS67x",
0x6355 : "962lua",
0x6787 : "Smart Link 56K Voice Modem (download from driverguide.com)",
0x6972 : "",
0x7001 : "SiS 7001 PCI to USB Open Host Controller ",
0x7002 : "USB 2.0 Enhanced Host Controller",
0x7005 : "Memory Stick Controller",
0x7007 : "OHCI Compliant FireWire Controller",
0x7012 : "SiS 7012 Audio Device / Realtek AC'97 Audio",
0x7013 : "Smart Link 56K Voice Modem (download from driverguide.com)",
0x7013 : "Smart Link 56K Voice Modem",
0x7015 : "Software Audio dd",
0x7016 : "10/100 Ethernet Adapter",
0x7018 : "Onboard audio",
0x7019 : "Hardware Audio",
0x7300 : "GUI Accelerator+3D",
0x7502 : "Realtek HDA Audio Driver.",
0x8139 : "2012",
0x9632 : "sis 650 integrated gfx controller (IGP)",
0x964 : "LPC BRIDGE",
0x9876 : "pci vga card for win95 & nt4 only",
0x9989 : "Smart Link 56K Voice Modem (download from driverguide.com)",
0x7012 : "PCI Audio Accelerator",
5811 : "",
},
0x103B : { 0x103b : "LAN Controller with 82562EM/EX PHY",
},
0x103C : { 0x0024 : "Standard Vista USB Keyboard",
0x0180 : "HID Keyboard Device",
0x0A01 : "HP Scanjet 2400",
0x1005 : "Visialize EG",
0x1008 : "001",
0x100A : "Hewlett-Packard VisualizeFX Series Video",
0x1028 : "HP ProtectSmart Hard Drive Protection - HP 3D DriveGuard",
0x1029 : "Tachyon XL2 Fibre Channel Adapter",
0x102A : "Tachyon TS Fibre Channel Host Adapter",
0x1030 : "DeskDirect 10/100VG LAN Adapter",
0x1031 : "DeskDirect 10/100 NIC",
0x1040 : "DeskDirect 10BaseT NIC",
0x1041 : "DeskDirect 10/100VG NIC",
0x1042 : "DeskDirect 10BaseT/2 NIC",
0x1048 : "",
0x1049 : "",
0x104A : "intel",
0x104B : "",
0x104D : "EL-10 Ethernet Adapter",
0x1064 : "PCnet Ethernet Controller",
0x10C1 : "NetServer Smart IRQ Router",
0x10ED : "HP Communications Port",
0x1200 : "10/100 NIC",
0x1219 : "NetServer PCI Hot-Plug Controller",
0x121A : "NetServer SMIC Controller",
0x121B : "NetServer Legacy COM Port Decoder",
0x121C : "NetServer PCI COM Port Decoder",
0x1229 : "System Bus Adapter",
0x122A : "I/O Controller",
0x122B : "Local Bus Adapter",
0x12FA : "Broadcom Wireless miniPCI in a HP laptop",
0x1302 : "HP Management Shared Memory Device",
0x137a : "Atheros AR5007",
0x1411 : "HP PSC 750",
0x171d : "HP Integrated Module with Bluetooth Wireless",
0x1F1D : "3G Broadband device",
0x201D : "3G Broadband device",
0x231D : "HP Integrated Module with Bluetooth Wireless Technology",
0x241D : "HP compaq nx6125",
0x2910 : "PCI Bus Exerciser",
0x292 : "PCI Host Interface Adapter",
0x2920 : "Fast Host Interface",
0x2924 : "PCI Host Interface Adapter",
0x2925 : "32 bit PCI Bus Exerciser and Analyzer",
0x2926 : "64 bit PCI Bus Exerciser and Analyzer",
0x2927 : "64 Bit",
0x294 : "pci hostinterface",
0x2940 : "64 bit",
0x311d : "ATHEROS AR3011 bluetooth 3.0+HS adapter",
0x3206 : "Adaptec Embedded Serial ATA HostRAID",
0x3207 : "not sure",
0x3220 : "P600 SmartArray Raid Controller",
0x3230 : "Smart Array P400 Controller",
0x323A : "Smart Array P410i Controller",
0x3302 : "Integrated Lights Out 2.0",
0x3A1D : "HP hs2340 HSPA+ MobileBroadband",
0x5461 : "HP integrated Module with Bluetooth 2.0 Wireless support",
0x9876 : "ATHEROS AR3011 bluetooth 3.0+HS adapter",
},
0x1043 : { 0x0675 : "Crestline",
0x1969 : "Attansic L1 Gigabit Ethernet 10/100/1000Base-T Adapter",
0x5653 : "ATI Radeon 3000 Graphics (Microsoft Corporation - WDDM v1.1)",
0x8103 : "NV31 [GeForce FX 5600 Ultra]",
0x82c6 : "Gigabit Ethernet(NDIS 6.0)",
},
0x1044 : { 0x1012 : "RAID Engine",
0x800A : "802.11 bg WLAN",
0xA400 : "SmartCache III/RAID SCSI Controller",
0xA500 : "PCI Bridge",
0xA501 : "I2O SmartRAID V Controller",
0xA511 : "SmartRAID Controller",
},
0x1045 : { 0x0005 : "",
0xA0F8 : "PCI USB Controller",
0xC101 : "GUI Accelerator",
0xC178 : "pci usb card 2- port",
0xC556 : "Viper",
0xC557 : "CPU Bridge (Viper)",
0xC558 : "ISA Bridge w/PnP",
0xC567 : "Vendetta chipset: host bridge",
0xC568 : "Vendetta chipset: ISA bridge",
0xC569 : "Pentium to PCI Bridge",
0xC621 : "PCI IDE Controller (PIC)",
0xC700 : "82C700 FireStar PCI to ISA Bridge",
0xC701 : "FireStar mobile chipset: host bridge",
0xC814 : "FireBridge II Docking Station Controller",
0xC822 : "CPU to PCI & PCI to ISA PnP bridge",
0xC824 : "FireFox 32-Bit PC Card Controller",
0xC825 : "PCI-to-ISA Bridge",
0xC832 : "CPU-to-PCI and PCI-to-ISA Bridge",
0xC861 : "FireLink PCI-to- 5 x USB Bridge( usb1.1 )",
0xC881 : "FireLink 1394 OHCI Link Controller",
0xC895 : "",
0xC931 : "ISA Sound & Game Port controller.",
0xC935 : "MachOne integrated PCI audio processor",
0xD568 : "PCI bus master IDE controller",
0xD768 : "Ultra DMA IDE controller",
},
0x1046 : { 0x5600 : "00/4&1a671",
},
0x1048 : { 0x0253 : "ELSA GLADIAC 528",
0x0C60 : "NVidia Geforce 2 MX",
0x0C71 : "NVidia GeForce3 Ti 200",
0x1000 : "ISDN Controller",
0x3000 : "",
0x8901 : "ELSA GLoria XL",
},
0x104A : { 0x0008 : "diamond",
0x0009 : "",
0x0010 : "PowerVR KYRO series 3 graphics processor",
0x0123 : "SPEAr1300",
0x0209 : "North/South Bridges",
0x020A : "North Bridge",
0x0210 : "ISA Bridge",
0x021A : "ISA Bridge",
0x021B : "ISA Bridge",
0x0228 : "IDE Controller",
0x0230 : "USB Controller",
0x0500 : "ADSL",
0x0981 : "10/100 Ethernet Adapter",
0x1746 : "mp280",
0x2774 : "PCI 10/100 Ethernet Controller",
0x3520 : "MPEG-II Video Decoder",
0x7108 : "Advanced HD AVC decoder with 3D graphics acceleration",
0xCC00 : "ConneXt I/O Hub multifunction device",
0xCC01 : "ConneXt I/O Hub multifunction device",
0xCC02 : "ConneXt I/O Hub multifunction device",
0xCC03 : "ConneXt I/O Hub multifunction device",
0xCC04 : "ConneXt I/O Hub multifunction device",
0xCC05 : "ConneXt I/O Hub multifunction device",
0xCC06 : "ConneXt I/O Hub multifunction device",
0xCC07 : "ConneXt I/O Hub multifunction device",
0xCC08 : "ConneXt I/O Hub multifunction device",
0xCC09 : "ConneXt I/O Hub multifunction device",
0xCC0A : "ConneXt I/O Hub multifunction device",
0xCC0B : "ConneXt I/O Hub multifunction device",
0xCC0C : "ConneXt I/O Hub multifunction device",
0xCC0D : "ConneXt I/O Hub multifunction device",
0xCC0E : "ConneXt I/O Hub multifunction device",
0xCC0F : "ConneXt I/O Hub multifunction device",
0xCC10 : "ConneXt I/O Hub multifunction device",
0xCC11 : "ConneXt I/O Hub multifunction device",
0xCC12 : "ConneXt I/O Hub multifunction device",
0xCC13 : "ConneXt I/O Hub multifunction device",
0xCC14 : "ConneXt I/O Hub multifunction device",
0xCC15 : "ConneXt I/O Hub multifunction device",
0xCC16 : "ConneXt I/O Hub multifunction device",
0xCC17 : "ConneXt I/O Hub multifunction device",
0xCD00 : "SPEAr1300",
0xCD80 : "Root Complex of SPEAr1300",
},
0x104B : { 0x1040 : "BT958 SCSI Host Adaptor",
0x8130 : "Flashpoint LT",
},
0x104C : { 0x803B : "Texas Instruments Card Reader",
0x014e : "4515",
0x0500 : "ThunderLAN 100 Mbit LAN Controller",
0x0508 : "PCI interface for TI380 compressors",
0x1000 : "",
0x104C : "PCI Simple Communications Controller",
0x3B04 : "otros dispositivos",
0x3D04 : "Permedia",
0x3D07 : "AGP Permedia 2",
0x8000 : "LYNX IEEE1394 FireWire Host Controller",
0x8009 : "OHCI-Lynx PCI IEEE 1394 Host Controller",
0x8010 : "OHCI-Lynx IEEE 1394 Host Controller",
0x8011 : "OHCI-Lynx IEEE 1394 Controller",
0x8017 : "OHCI-Lynx IEEE 1394 Controller",
0x8019 : "OHCI-Lynx PCI IEEE 1394 Host Controller",
0x8020 : "OHCI-Lynx PCI IEEE 1394 Host Controller",
0x8021 : "1394a-2000 OHCI PHY/Link Layer CONTROLLER",
0x8023 : "IEEE1394a-2000 OHCI PHY/Link-Layer Ctrlr",
0x8024 : "1394a-2000 OHCI PHY/Link Layer Ctrl",
0x8025 : "1394b OHCI-Lynx IEEE 1394 Host Controller",
0x8026 : "1394a-2000 OHCI PHY/Link Layer Ctrlr",
0x8027 : "OHCI-Lynx IEEE 1394 Controller",
0x8029 : "OHCI Compliant IEEE-1394 FireWire Controller ",
0x802e : "OHCI Compliant IEEE 1394 Host Controller",
0x8033 : "Integrated FlashMedia ",
0x8034 : "SDA Standard Compliant SD Host Controller",
0x8035 : "PCI GemCore based SmartCard controller",
0x8036 : "Texas Instruments PCIxxx12 Cardbus Controller",
0x8038 : "Texas Instruments PCI GemCore based SmartCard Controller",
0x8039 : "104C",
0x803a : "OHCI Compliant IEEE 1394 Host controller",
0x803B : "Texas Instruments Card Reader",
0x803c : "SDA Standard Compliant SD Host Controller",
0x803D : "Texas Instruments PCI GemCore based SmartCard controller",
0x8119 : "iRDA Compatible Controller",
0x8201 : "TI UltraMedia Firmware Loader Device",
0x8204 : " 4515",
0x8231 : "PCI-Express to PCI/PCI-X bridge",
0x8232 : "Controladora de vdeo multimedia",
0x8241 : "Texas Instruments USB 3.0 XHCI Host Controller",
0x8400 : "D-Link AirPlus DWL-520+",
0x8671 : "bogus",
0x9065 : "Fixed Point Digital Signal Processor",
0x9066 : "U.S. Robotics 802.11g Wireless Turbo PC Card ",
0xA001 : "64-bit PCI ATM SAR",
0xA100 : "32-bit PCI ATM SAR",
0xA102 : "HyperSAR Plus w/PCI host & UTOPIA i/f",
0XA106 : "Fixed Point Digital Signal Processor",
0xA186 : "TI C6416T DSP",
0xa828 : "PCI-to-PCI Bridge",
0xAC10 : "PC Card Controller",
0xAC11 : "PC Card Controller",
0xAC12 : "PC card CardBus Controller",
0xAC13 : "Texas Instruments PCIxx12 Integrated FlashMedia Controller",
0xAC15 : "CardBus Controller",
0xAC16 : "PC Card CardBus Controller",
0xAC17 : "CardBus Controller",
0xAC18 : "PC card CardBus Controller",
0xAC19 : "PC card CardBus Controller",
0xAC1A : "PC card CardBus Controller",
0xAC1B : "PC card CardBus Controller",
0xAC1C : "PC Card CardBus Controller",
0xac1e : "PCI To PCMCIA bridge",
0xAC1F : "PC card CardBus Controller",
0xAC20 : "PCI to PCI Bridge",
0xAC21 : "PCI to PCI Bridge",
0xAC22 : "PCI Docking Bridge",
0xAC23 : "PCI-to-PCI Bridge",
0xAC28 : "PCI-to-PCI Bridge",
0xAC30 : "PC card CardBus Controller",
0xAC40 : "PC card CardBus Controller",
0xAC41 : "PC card CardBus Controller",
0xAC42 : "PC card CardBus Controller",
0xAC43 : "PC card CardBus Controller",
0xAC44 : "PC Card Controller SDFSDAFSADFSDAFSDAF",
0xAC46 : "PCCard CardBus Controller",
0xac47 : "Cardbus",
0xAC50 : "PC card cardBus Controller",
0xAC51 : "Texas Instruments 1420",
0xAC52 : "PC card CardBus Controller",
0xAC53 : "PC card CardBus Controller - 5-in-1 Media Card Reader",
0xAC54 : "PCCard CardBus Controller w/UltraMedia",
0xAC55 : "PCCard CardBus Controller",
0xAC56 : "PCCard CardBus Controller",
0xAC57 : "PCCard CardBus Controller",
0xAC58 : "PCCard CardBus Controller",
0xAC59 : "PCCard CardBus Controller w/UltraMedia",
0xAC5A : "PCCard CardBus Controller w/UltraMedia",
0xac60 : "PCI2040 PCI to DSP Bridge",
0xac8e : "Generic CardBus Controller ",
0xAC8F : "FlashMedia",
0xB000 : "Device ID: 0xB001 ",
0xB001 : "DSP with a C64x+ core and M/S PCI interface",
0xFE00 : "FireWire Host Controller",
0xFE03 : "FireWire Host Controller",
},
0x104D : { 0x011B : "USB Ralink Wireless LAN",
0x5001 : "Sony Firmware Extension Parser listed as ACPI\SNY5001 in device manager.",
0x8009 : "PCI bus 13",
0x8039 : "OHCI i.LINK (IEEE 1394) PCI Host Ctrlr",
0x8056 : "Rockwell HCF 56K Modem",
0x8087 : "SONY MPEG ENCODER",
0x808A : "Memory Stick Controller",
},
0x104E : { 0x0017 : "",
0x0107 : "Spitfire VGA Accelerator",
0x0109 : "Video Adapter",
0x0217 : "",
0x0317 : "",
0x0611 : "T9732",
0x317 : "Spitfire VGA Accelerator",
},
0x104F : { 0x104F : "Multi I/O",
},
0x1050 : { 0x6692 : "PCI BusISDN S/T-Controller",
0x0000 : "Ethernet Controller (NE2000 compatible)",
0x0001 : "PCI/IDE controller",
0x0033 : "Winbond W89C33 mPCI 802.11 Wireless LAN Adapter",
0x0105 : "Ethernet Adapter",
0x0628 : "PCI to ISA Bridge Set",
0x0840 : "100/10Mbps Ethernet Controller",
0x0940 : "winbond pci ethernet",
0x1050 : "Video capture card mpeg-1",
0x5A5A : "ELANC-PCI Twisted-pair Ether-LAN Ctrlr",
0x6692 : "PCI BusISDN S/T-Controller",
0x8481 : "SD Host Controller",
0x9921 : "MPEG1 capture card",
0x9922 : "MPEG-1/2 Decoder",
0x9960 : "Video Codec",
0x9961 : "H.263/H.261 Video Codec",
0x9970 : "VGA controller",
0x9971 : "W9971CF",
6692 : "",
},
0x1051 : { 0x0100 : "",
},
0x1054 : { 0003 : "0003",
0x0001 : "PCI Bridge",
0x0002 : "PCI bus Cntrlr",
0x0003 : "hts547575a9e384",
0x3505 : "SuperH (SH) 32-Bit RISC MCU/MPU Series",
},
0x1055 : { 0x0810 : "EFAR 486 host Bridge",
0x0922 : "Pentium/p54c host Bridge",
0x0926 : "ISA Bridge",
0x9130 : "Ultra ATA/66 IDE Controller",
0x9460 : "Victory66 PCI to ISA Bridge",
0x9461 : "Victory66 UDMA EIDE Controller",
0x9462 : "Victory66 USB Host Controller",
0x9463 : "Victory66 Power Management Controller",
0xe420 : "PCI 10/100 Ethernet controller",
},
0x1056 : { 0x2001 : "Philips P89C51RD271BA. 1D041700A0. AeD0217G",
},
0x1057 : { 0*5600 : "Motorola FM 56 PCI Speakerphone Modem",
0x0001 : "PCI Bridge / Memory Controller (PCIB/MC)",
0x0002 : "PCI Bridge/Memory Controller (PCIB/MC)",
0x0003 : "Integrated Processor",
0x0004 : "PCI Bridge/Memory Controller for PPC",
0x0006 : "Integrated Processor",
0x0100 : "HCF-PCI",
0x0431 : "100VG Ethernet Controller",
0x1801 : "24-bit Digital Signal Processor",
0x1802 : "24-Bit Digital Signal Processor",
0x18C0 : "PowerQUICC II PCI Bridge",
0x3052 : "MotorolaSM56Modem_PCI device",
0x3055 : "Motorola SM56 Data Fax Modem ",
0x3057 : "Modem Device on High Definition Audio Bus",
0x3410 : "Digital Signal Processor",
0x3421 : "Modem",
0x4801 : "PowerPC Chipset",
0x4802 : "memory control chipset",
0x4803 : "",
0x4806 : "",
0x4809 : "HotSwap Controller",
0x5600 : "SM 56 PCI Speakerphone/Data",
0x5602 : "PCI Modem",
0x5608 : "Motorola SM56 Speakerphone Modem",
0x5803 : "32-Bit Embedded PowerPC Processor",
0x6400 : "Security Co-Processor",
0x9876 : "3052",
},
0x105A : { 0x0262 : "Ultra66/FastTrak66",
0x0D30 : "MBUltra100/MBFastTrack100 Lite",
0x0D38 : "FastTrak66 Lite EIDE Controller",
0x105A : "EIDE Controller",
0x1275 : "MBUltra133",
0x1960 : "SuperTrak 66/100 RAID",
0x1962 : "SuperTrak SX 6000",
0x3318 : "SATA150 TX4",
0x3319 : "FastTrak S150 TX4",
0x3371 : "FastTrak S150 TX2+",
0x3373 : "FastTrak 378/SATA 378 RAID Controller",
0x3375 : "SATA150 TX2+",
0x3376 : "FastTrak 376 Controller",
0x3515 : "FastTrak TX43xx",
0x3519 : "FastTrak TX42xx",
0x3570 : "FastTrak TX2300 SATA300 Controller",
0x3571 : "Fasttrack TX2200",
0x3574 : "SATAII 150 579",
0x3d17 : "SATA 300 TX4 Controller",
0x3D18 : "SATAII 150TX2+/SATAII150 TX4",
0x3D73 : "SATAII 300 TX2+",
0x3F19 : "FastTrak TX2650/4650/4652",
0x3F20 : "FastTrak TX2650(3F21)/4650(3F22)/PDC42819(3716)",
0x4302 : "SuperTrak EX 43X0",
0x4303 : "SuperTrak EX 4350",
0x4D30 : "FastTrack100 on Intel MB SE7500CW2",
0x4D33 : "FastTrak/Ultra33 ATA RAID controller",
0x4D38 : "Ultra66/FastTrak66",
0x4D68 : "Ultra100TX2/FastTrak100TX/LP",
0x4D69 : "Ultra133TX2",
0x5275 : "MBUltra133/MBFastTrak133",
0x5300 : "EIDE Controller",
0x6268 : "FastTrak100 TX2/TX4/LP",
0x6269 : "FastTrak TX2000 EIDE controller",
0x6300 : "FastTrak SX 8300",
0x6301 : "FastTrak SX8300-1",
0x6302 : "FastTrak SX 4300",
0x6303 : "FastTrak SX 4",
0x6304 : "FastTrak SX8300-2",
0x6305 : "FastTrak SX8300-3",
0x6306 : "FastTrak SX 4300-2",
0x6307 : "FastTrak SX 4300-3",
0x6621 : "FastTrak SX4000",
0x6622 : "FastTrak S150SX4",
0x6629 : "FastTrak TX4000",
0x7250 : "Vitesse 7250 SAS RAID",
0x7275 : "SBUltra133/SBFastTrak 133 Lite",
0x8000 : "SATAII150 SX8",
0x8002 : "SATAII150 SX8",
0x8003 : "FastTrak SX4000",
0x8004 : "SATAII150 SX8",
0x8006 : "SATAII150 SX8",
0x8350 : "SuperTrak EX8350/16350/8300/16300",
0x8650 : "SuperTrak EX SAS RAID",
0xC350 : "SuperTrak EX 123X0",
0xE350 : "SuperTrak EX 243X0",
},
0x105D : { 0x2309 : "GUI Accelerator",
0x2339 : "Imagine 128 Series 2",
0x493D : "Revolution 3D",
0x5348 : "Revolution IV",
},
0x1060 : { 0x0001 : "486 Chipset",
0x0002 : "ISA Bridge",
0x0101 : "EIDE Controller",
0x0881 : "HB4 486 PCI Chipset",
0x0886 : "ISA Bridge",
0x0891 : "Pentium CPU to PCI bridge",
0x1001 : "IDE Cntrlr (dual function)",
0x673A : "EIDE Controller",
0x673B : "EIDE Master/DMA",
0x8710 : "VGA Cntrlr",
0x8821 : "CPU/PCI Bridge",
0x8822 : "PCI/ISA Bridge",
0x8851 : "Pentium CPU/PCI Bridge",
0x8852 : "Pentium CPU/ISA Bridge",
0x886A : "ISA Bridge with EIDE",
0x8881 : "HB4 486 PCI Chipset",
0x8886 : "ISA Bridge (w/o IDE support)",
0x888A : "",
0x8891 : "586 Chipset",
0x9017 : "Ethernet",
0x9018 : "Ethernet",
0x9026 : "Fast Ethernet",
0xE881 : "486 Chipset",
0xE886 : "ISA Bridge w/EIDE",
0xE88A : "PCI / ISA Bridge",
0xE891 : "um8891n",
},
0x1061 : { 0x0001 : "GUI Accelerator",
0x0002 : "MPEG Decoder",
},
0x1065 : { 0x8139 : "Realtek 8139C Network Card",
},
0x1066 : { 0x0000 : "VL Bridge",
0x0001 : "Vesuvius V1-LS System Controller",
0x0002 : "Vesuvius V3-LS ISA Bridge",
0x0003 : "Nile PCI to PCI Bridge",
0x0004 : "Nile-II PCI to PCI Bridge",
0x0005 : "System Controller",
0x8002 : "ISA Bridge",
},
0x1067 : { 0x1002 : "VolumePro Volume Rendering Accelerator",
},
0x106B : { 0x0001 : "PowerPC Host-PCI Bridge",
0x0002 : "I/O Controller",
0x0003 : "",
0x0004 : "Video-in",
0x0007 : "I/O Controller",
0x0009 : "BCM5703X",
0x000C : "",
0x000E : "Mac I/O Controller",
0x0010 : "Mac I/O Controller",
0x0017 : "Mac I/O Controller",
0x0018 : "FireWire Controller",
0x001F : "Host-PCI bridge",
0x0020 : "AGP interface",
0x0026 : "USB Interface",
0x0027 : "AGP interface",
0x002D : "AGP Bridge",
0x002E : "PCI Bridge",
0x002F : "Internal PCI",
0x0030 : "FireWire Controller",
0x003B : "Integrated ATA Controller",
0x004f : "Mac I/O controler",
0x0050 : "IDE controler",
0x0051 : "Sungem ethernet controler",
0x0052 : "Firewire controler",
0x0053 : "PCI Bridge",
0x0054 : "PCI Bridge",
0x0055 : "PCI Bridge",
0x0058 : "AGP Bridge",
0x008A : "Mac Pro RAID Card",
0x008C : "AirPort Extreme",
},
0x106C : { 0x8801 : "Dual Pentium ISA/PCI Motherboard",
0x8802 : "PowerPC ISA/PCI Motherboard",
0x8803 : "Dual Window Graphics Accelerator",
0x8804 : "PCI LAN Controller",
0x8805 : "100-BaseT LAN Controller",
},
0x106E : { 0x4362 : "Yukon PCI-E Gigabit Ethernet Controller (copper)",
},
0x1073 : { 0x0001 : "3D graphics Cntrlr",
0x0002 : "RPA3 3D-Graphics Controller",
0x0003 : "",
0x0004 : "PCI Audio Controller",
0x0005 : "DS1 Audio",
0x0006 : "DS1 Audio",
0x0008 : "DS1 Audio",
0x000A : "DS-1L PCI Audio Controller",
0x000C : "DS-1L PCI audio controller",
0x000D : "YamahaDS1 native audio ",
0x0010 : "DS-1 PCI audio controller",
0x0012 : "DS-1E PCI Audio Controller",
0x0020 : "DS-1 Audio",
0x1000 : "Sound system",
0x2000 : "Digital Mixing Card",
0x9876 : "yamaha",
},
0x1074 : { 0x4E78 : "Nx586 Chipset",
},
0x1077 : { 0x1016 : "Single Channel Ultra3 SCSI Processor",
0x1020 : "Fast-wide SCSI - Sparc PCI",
0x1022 : "Fast-wide SCSI",
0x1080 : "SCSI Host Adapter",
0x1216 : "Dual Channel Ultra3 SCSI Processor",
0x1240 : "SCSI Host Adapter",
0x1280 : "SCSI Host Adapter",
0x2020 : "Fast!SCSI Basic Adapter",
0x2100 : "64-bit Fibre Channel Adapter",
0x2200 : "PCI Fibre Channel Adapter",
0x2300 : "64-bit PCI FC-AL Adapter",
0x2312 : "Fibre Channel Adapter",
0x2422 : "QLogic PCI to Fibre Channel Host Adapter for QLA2460",
0x2432 : "4Gb PCI Single/Dual Fibre Channel HBA",
0x2532 : "8Gb PCIe x8 Single/Dual Fibre Channel HBA",
0x3010 : "n/a",
0x3032 : "QLOGIC Dual Port 1GBPS PCI-E HBA",
0x4000 : "",
0x4010 : "",
0x6312 : "Qlogic FC-HBA QLA200",
0x6422 : "4-Gbps Fibre Channel to PCI-X 2.0 266MHz controller for Embedded Applications",
0x6432 : "4-Gbps Fibre Channel to PCIe controller for Embedded Applications",
0x8000 : "QLE8142 QLogic PCI Express to 10 GbE Dual Channel CNA",
0x8001 : "QLE8142 QLogic PCI Express to 10 GbE Dual Channel CNA (FCoE)",
0x8020 : "QLogic Dual Port 10 Gigabit Ethernet CNA",
0x8021 : "QLogic [FCoE] Adapter",
0x8022 : "QLE8142 QLogic PCI Express to 10 GbE Dual Channel CNA (iSCSI)",
},
0x1078 : { 0x0000 : "ISA Bridge",
0x0001 : "Cyrix Integrated CPU",
0x0002 : "ISA Bridge",
0x0100 : "ISA bridge",
0x0101 : "SMI status and ACPI timer",
0x0102 : "IDE Controller",
0x0103 : "XpressAUDIO",
0x0104 : "Video Controller",
0x0400 : "CPU to PCI Bridge",
0x0401 : "Power Management Controller",
0x0402 : "IDE Controller",
0x0403 : "Expansion Bus",
},
0x1079 : { 0x0d01 : "",
0x10de : "zdzvz",
},
0x107D : { 0x0000 : "Graphic GLU-Logic",
},
0x107E : { 0x0001 : "FRED Local Bus I/F to PCI Peripheral",
0x0002 : "100 vg anylan Cntrlr",
0x0004 : "Fibre Channel Host Adapter",
0x0005 : "Fibre Channel Host Adapter",
0x0008 : "(i)chipSAR+ 155 MBit ATM controller",
0x9003 : "",
0x9007 : "",
0x9008 : "",
0x900C : "",
0x900E : "",
0x9011 : "",
0x9013 : "",
0x9023 : "",
0x9027 : "",
0x9031 : "",
0x9033 : "Adapter",
0x9060 : "CompactPCI T1/E1/J1Communications Ctrlr",
0x9070 : "PMC T1/E1/J1 Communications Controller",
0x9080 : "PMC ATM Over OC-3/STM-1 Comm Controller",
0x9081 : "PMC ATM Over OC-3/STM-1 Comm Controller",
0x9082 : "PMC ATM Over OC-3/STM-1 Comm Controller",
0x9090 : "PMC ATM Over T3/E3 Communications Ctrlr",
0x90A0 : "PMC Quad T1/E1/J1 Communications Ctrlr",
},
0x107F : { 0x0802 : "pinacale capture card",
0x0803 : "EIDE Bus Master Controller",
0x0806 : "EIDE Controller",
0x2015 : "EIDE Controller",
},
0x1080 : { 0x0600 : "CPU to PCI & PCI to ISA Bridge",
0xC691 : "AN2131QC 0230",
0xC693 : "PCI to ISA Bridge",
},
0x1081 : { 0x0D47 : "Radius PCI to NuBUS Bridge",
},
0x1083 : { 0x0001 : "PCI Enhanced IDE Adapter",
0x0613 : "PCI",
},
0x1085 : { 0x0001 : "Datalaster Interface for OBD automotive",
},
0x1087 : { 0x9200 : "",
},
0x1089 : { 0x5555 : "3249",
},
0x108A : { 0x0001 : "PCI-VME Bus Adapter",
0x0003 : "PCI to VME Bridge",
0x0010 : "VME Bridge",
0x0040 : "",
0x3000 : "VME Bridge",
},
0x108D : { 0x0001 : "Token-Ring 16/4 PCI Adapter",
0x0002 : "Fastload 16/4 PCI/III Token Ring Adapter",
0x0004 : "RapidFire Token Ring 16/4 Adapter",
0x0005 : "GoCard Token Ring 16/4 Adapter",
0x0006 : "RapidFire Token Ring 100 Adapter",
0x0007 : "RapidFire Token Ring 16/4 Adapter",
0x0008 : "RapidFire HSTR 100/16/4 Adapter",
0x000A : "RapidFire Token-Ring 16/4 PCI Adapter",
0x0011 : "Ethernet Controller",
0x0012 : "Ethernet PCI/II 10/100 Controller",
0x0013 : "PCI/II Ethernet Controller",
0x0014 : "Ethernet PCI/II 10/100 Controller",
0x0019 : "10/100 Ethernet Controller",
0x0021 : "155 Mbit ATM Adapter",
0x0022 : "ATM Adapter",
},
0x108E : { 0x0001 : "",
0x1000 : "PCI Input/Output Controller",
0x1001 : "Happy Meal Ethernet",
0x1100 : "",
0x1101 : "",
0x1102 : "",
0x1103 : "",
0x2BAD : "Sun Gigabit Ethernet Card",
0x5000 : "UltraSPARC-IIi Advanced PCI Bridge",
0x5043 : "Co-processor",
0x7063 : "PCI card with Intel or AMD processor",
0x8000 : "UPA to PCI Interface (UPA)",
0x8001 : "PCI Bus Module",
0xA000 : "Sabre",
0xA001 : "Hummingbird",
0xabba : "10/100/1000 Ethernet adapter",
},
0x1091 : { 0x0020 : "3D Graphics Processor",
0x0021 : "3D graphics processor w/texturing",
0x0040 : "3D graphics frame buffer",
0x0041 : "3D graphics frame buffer",
0x0060 : "Proprietary bus Bridge",
0x00E4 : "",
0x0720 : "Motion JPEG Codec",
},
0x1092 : { 0x00A0 : "GUI Accelerator",
0x00A8 : "GUI Accelerator",
0x0550 : "",
0x08D4 : "WinModem",
0x094C : "SupraExpress 56i Pro",
0x09C8 : "SupraExpress 56i Pro VCC",
0x1002 : "RS56-pci",
0x1092 : "2710a",
0x6120 : "DVD",
0x8810 : "GUI Accelerator",
0x8811 : "GUI Accelerator",
0x8880 : "",
0x8881 : "GUI Accelerator",
0x88B0 : "GUI Accelerator",
0x88B1 : "GUI Accelerator",
0x88C0 : "GUI Accelerator",
0x88C1 : "GUI Accelerator",
0x88D0 : "GUI Accelerator",
0x88D1 : "GUI Accelerator",
0x88F0 : "GUI Accelerator",
0x88F1 : "GUI Accelerator",
0x9876 : "Supra Express 56i Pro CW #2",
0x9999 : "Diamand Technology DT0398",
},
0x1093 : { 0x0160 : "data adquisition input and output",
0x0161 : "Multifunction data acquisition board",
0x0162 : "24MIO 6-03-2",
0x1150 : "High Speed Digital I/O Board",
0x1170 : "",
0x1180 : "base system device",
0x1190 : "",
0x11B0 : "",
0x11C0 : "",
0x11D0 : "",
0x11E0 : "",
0x1270 : "Multifunction Data Acquisition Card",
0x12b0 : "High Speed DIO",
0x1310 : "Data Acquisition Device",
0x1320 : "",
0x1330 : "",
0x1340 : "Multifunction Data Acquisition Card",
0x1350 : " NI PCI-6071E Multifunction I/O & NI-DAQ",
0x1360 : "",
0x17D0 : "",
0x18B0 : "",
0x28b0 : "I/O Terminal NI-DAQ (Legacy) and NI-DAQmx",
0x2A60 : "",
0x2A70 : "Multifunction Data Acquisition Card",
0x2A80 : "Multifunction Data Acquisition Card",
0x2B20 : "",
0x2C80 : "",
0x2CA0 : "PCI-6034E",
0x702C : "NI FPGA Modul",
0x70af : "16-Bit",
0x70b8 : "Multifunction DAQ Device",
0x70E3 : "NI PXI-8431/8 (RS485/RS422)",
0x70E4 : "NI PCI-8430/8 (RS-232) Interface",
0x710e : "GPIB Controller Interface Board",
0x71BC : "16-Bit",
0x7414 : "NI PCIe-GPIB+ GPIB with analyzer",
0xB001 : "",
0xB011 : "",
0xB021 : "",
0xB031 : "",
0xB041 : "1pcs",
0xB051 : "",
0xB061 : "",
0xB071 : "IMAQ-PCI-1422",
0xB081 : "",
0xB091 : "bluethooth",
0xC801 : "GPIB Controller Interface Board",
0xC811 : "",
0xC821 : "",
0xC831 : "PCI-GPIB",
0xC840 : "",
0xd130 : "2-port RS-232 Serial Interface Board",
},
0x1095 : { 0x0240 : "SIL3112",
0x0242 : "SIL3132",
0x0244 : "SIL3132",
0x0640 : "PCI0640A/B",
0x0641 : "pci0640",
0x0642 : "PCI0642",
0x0643 : "PCI0643",
0x0646 : "CMD646",
0x0647 : "PCI0647",
0x0648 : "PCI-648",
0x0649 : "PCI-649",
0x0650 : "PBC0650A",
0x0670 : "USB0670",
0x0673 : "USB0673",
0x0680 : "SiI 0680/680A",
0x1392 : "1390/1392",
0x2455 : "SI3124",
0x3112 : "SIL3112",
0x3114 : "Sil 3114",
0x3124 : "SiI 3124",
0x3132 : "SiI 3132",
0x3512 : "Sil 3512",
0x3531 : "3531",
0x9876 : "0x9876",
},
0x1096 : { 0x1106 : "Realtek AC97 Audio for VIA (R) Audio Controller",
0x3059 : "South Bridge",
},
0x1097 : { 0x0038 : "EIDE Controller (single FIFO)",
},
0x1098 : { 0x0001 : "EIDE Controller",
0x0002 : "EIDE Controller",
},
0x109A : { 0x8280 : "4 channel video digitizer cardm",
},
0x109E : { 0x0350 : "rb8701.1",
0x0350 : "tv tuner driverhj",
0x0351 : "BrookTree Bt848 Video Capture Device - Audio Section PCI",
0x0369 : "Video Capture",
0x036C : "",
0x036E : "AVerMediaAverTV WDM AudioCapture (878)",
0x036E : "Video Capture",
0x036E : "Video Capture",
0x036F : "Video Capture",
0x0370 : "Video Capture (10 bit High qualtiy cap)",
0x0878 : "AVerMediaAverTV WDM AudioCapture (878)",
0x0879 : "Video Capture (Audio Section)",
0x0880 : "Video Capture (Audio Section)",
0x109E : "Multimedia Video Controllerm",
0x109E : "0400 video devce",
0x2115 : "BtV Mediastream Controller 9x",
0x2125 : "BtV Mediastream Controller",
0x2164 : "Display Adapter",
0x2165 : "MediaStream Controller",
0x36e : "25878-13",
0x36E : "Brooktree Corp",
0x36E : "conexant 878a",
0x8230 : "ATM Segment/Reassembly Controller (SRC)",
0x8472 : "32/64-channel HDLC Controllers",
0x8474 : "128-channel HDLC Controller",
},
0x109F : { 0x036F : "Video Capturee",
},
0x10A4 : { 0X5969 : "",
},
0x10A8 : { 0x0000 : "ethernet controller",
},
0x10A9 : { 0x0004 : "",
0x0005 : "",
0x0006 : "",
0x0007 : "",
0x0008 : "",
0x0009 : "Gigabit Ethernet",
0x0010 : "Video I/O",
0x0011 : "",
0x0012 : "",
0x1001 : "",
0x1002 : "",
0x1003 : "",
0x1004 : "",
0x1005 : "",
0x1006 : "",
0x1007 : "",
0x1008 : "",
0x2001 : "Fibre Channel",
0x2002 : "",
0x8001 : "",
0x8002 : "",
},
0x10AB : { 0x1005 : "USB Pendrive",
0x1007 : "usb pendrive",
0x8086 : "PCI Simple Communications Controller ",
},
0x10AD : { 0x0001 : "EIDE Ctrlr",
0x0103 : "PCI-ide mode 4.5 Cntrlr",
0x0105 : "Sonata bus master PCI-IDE controller",
0x0565 : "PCI/ISA bridge",
},
0x10B5 : { 0x0324 : "",
0x0480 : "Integrated PowerPC I/O Processor",
0x0960 : "PCI Reference Design Kit for PCI 9080",
0x1030 : "ISDN card",
0x1054 : "dual channel ISDN card",
0x1078 : "Vision Systems VScom PCI-210",
0x1103 : "Vision Systems VScom PCI-200",
0x1146 : "Vision Systems VScom PCI-010S",
0x1147 : "Vision Systems VScom PCI-020S",
0x1151 : "ISDN card",
0x1152 : "ISDN card",
0x2724 : "Thales PCSM Security Card",
0x2748 : "TPCX Transientrecorder Card",
0x3001 : "gpscard",
0x5406 : "PCI Reference Design Kit for PLX PCI 9054",
0x5601 : "32-bit; 66MHz PCI Bus Master I/O Accelerator",
0x6520 : "PCI-X to PCI-X Bridge",
0x6ACC : "General Mechatronics 6 Axis Motion Control Card for EMC2",
0x8111 : "1 Lane PCI Express to PCI bridge (PEX8111); 1 Lane PCI Express to Generic Local Bus bridge (PEX8311)",
0x8112 : "1 Lane PCI Express to PCI bridge",
0x8508 : "8 Lane",
0x8509 : "8-lane PCI-Express Switch",
0x8516 : "Versatile PCI Express Switch",
0x8518 : "PLX PCI-e switch",
0x8532 : "Versatile PCI Express Switch",
0x8548 : "48-lane PCIe switch",
0x8609 : "8 Lane",
0x8664 : "64-Lane",
0x9030 : "PCI SMARTarget I/O Accelerator",
0x9036 : "Interface chip - value 1k",
0x9050 : "Target PCI Interface Chip - value 1k",
0x9052 : "PCI 9052 Target PLX PCI Interface Chip",
0x9054 : "PCI I/O Accelerator",
0x9056 : "32-bit",
0x9060 : "PCI Bus Master Interface Chip",
0x906D : "PCI Bus Master Interface Chip",
0x906E : "PCI Bus Master Interface Chip",
0x9080 : "High performance PCI to Local Bus chip",
},
0x10B6 : { 0x0001 : "Ringnode (PCI1b)",
0x0002 : "Ringnode (PCIBM2/CardBus)",
0x0003 : "Ringnode",
0x0004 : "Smart 16/4 Ringnode Mk1 (PCIBM1)",
0x0006 : "16/4 CardBus Adapter (Eric 2)",
0x0007 : "",
0x0009 : "Smart 100/16/4 PCi-HS Ringnode",
0x000A : "Smart 100/16/4 PCI Ringnode",
0x000B : "16/4 CardBus Adapter Mk2",
0x1000 : "ATM adapter",
0x1001 : "ATM adapter",
0x1002 : "ATM Adapter",
},
0x10B7 : { 0x0001 : "1000BaseSX Gigabit Etherlink",
0x0013 : "3Com11a/b/g Wireless PCI Adapter ",
0x1000 : "3COM 3C905CX-TXNM with 40-0664-003 ASIC",
0x1006 : "Broadcom Corporation NetXtreme BCM5701 Gigabit Ethernet",
0x1007 : "V.90 Mini-PCI Modem",
0x1700 : "Gigabit Ethernet PCI CODEC",
0x1F1F : "AirConnect Wireless LAN PCI Card",
0x3390 : "Token Link Velocity",
0x3590 : "TokenLink Velocity XL Adapter",
0x4500 : "Cyclone",
0x5055 : "Laptop Hurricane",
0x5057 : "Megahertz 10/100 LAN CardBus PC Card",
0x5157 : "Megahertz 10/100 LAN CardBus PC Card",
0x5257 : "Cyclone Fast Ethernet CardBus PC Card",
0x5900 : "Ethernet III Bus Fast PCI",
0x5920 : "PCI/EISA 10Mbps Demon/Vortex",
0x5950 : "100MB PCI Ethernet Adapter",
0x5951 : "Fast EtherLink PCI T4",
0x5952 : "Fast EtherLink PCI MII",
0x5970 : "PCI/EISA Fast Demon/Vortex",
0x5B57 : "Megahertz 10/100 LAN CardBus",
0x6055 : "10/100 Fast Ethernet MiniPCI Adapter",
0x6056 : "MiniPCI 10/100 Ethernet+Modem56k (see devid:1007)",
0x6560 : "Cyclone CardBus PC Card",
0x6561 : "10/100 LAN+56K Modem CardBus PC Card",
0x6562 : "Cyclone CardBus PC Card",
0x6563 : "10/100 LAN+56K Modem CardBus PC Card",
0x6564 : "Cyclone CardBus PC Card",
0x6565 : "Global 10/100 Fast Ethernet+56K Modem",
0x7646 : "3com",
0x7770 : "AirConnect Wireless PCI",
0x8811 : "Token Ring",
0x9000 : "Fast Etherlink PCI TPO NIC",
0x9001 : "Fast Etherlink XL PCI Combo NIC",
0x9004 : "EtherLink XL TPO 10Mb",
0x9005 : "Fast Etherlink 10Mbps Combo NIC",
0x9006 : "EtherLink XL TPC",
0x900A : "EtherLink PCI Fiber NIC",
0x9041 : "Fast Etherlink XL 10/100",
0x9050 : "Fast Etherlink XL PCI 10/100",
0x9051 : "Fast Etherlink XL 10/100",
0x9055 : "Fast Etherlink 10/100 PCI TX NIC",
0x9056 : "Fast EtherLink XL 10/100",
0x9058 : "Deluxe EtherLink 10/100 PCI Combo NIC",
0x905A : "Fast EtherLink 100 Fiber NIC",
0x9200 : "3Com 10/100 Managed NIC 3C905CX-TX-M",
0x9201 : "Integrated Fast Ethernet Controller",
0x9202 : "3C920B-EMB 3Com + Realtek 8201L",
0x9210 : "Integrated Fast Ethernet Controller",
0x9300 : "3ComSOHO100B-TX",
0x9800 : "Fast EtherLink XL Server Adapter2",
0x9805 : "Python-T 10/100baseTX NIC",
0x9876 : "3C920B-EMB 3Com + Realtek 8201L",
0x9902 : "EtherLink 10/100 PCI with 3XP Processor",
0x9903 : "EtherLink 10/100 PCI with 3XP Processor",
0x9905 : "100FX PCI Server NIC w/3XP",
0x9908 : "EtherLink 10/100 Server PCI with 3XP",
0x9909 : "EtherLink 10/100 Server PCI with 3XP",
0xD004 : "EtherLink XL PCI",
},
0x10B8 : { 0x0005 : "EPIC/XF 10/100 Mbps Fast Ethernet Ctrlr",
0x0006 : "EPIC/C Ethernet CardBus Integrated Ctrlr",
0x1000 : "FDC",
0x1001 : "FDC",
0xA011 : "Fast ethernet controller",
0xB106 : "CardBus Controller",
},
0x10B9 : { 0x0101 : "PCI Audio Device (OEM)",
0x0102 : "PCI Audio Device (OEM)",
0x0111 : "C-Media Audio Device (OEM)",
0x0780 : "Multi-IO Card",
0x0782 : "Multi-IO Card",
0x10b9 : "0402t505 CK46828100B",
0x10CE : "cpi",
0x1435 : "VL Bridge",
0x1445 : "CPU to PCI & PCI to ISA Bridge w/EIDE",
0x1449 : "ISA Bridge",
0x1451 : "Pentium CPU to PCI Bridge",
0x1461 : "P54C Chipset",
0x1489 : "486 PCI Chipset",
0x1511 : "Aladdin 2 Host Bridge",
0x1513 : "Aladdin 2 South Bridge",
0x1521 : "Bios",
0x1523 : "ISA Bridge",
0x1533 : "PCI South Bridge",
0x1535 : "ISA Bridge",
0x1541 : "Aladdin V AGPset Host Bridge",
0x1543 : "Aladdin V chipset South Bridge",
0x1561 : "North Bridge",
0x1563 : "South Bridge with Hypertransport Support",
0x1632 : "North Bridge",
0x1641 : "CPU to PCI Bridge",
0x1644 : "AGP System Controller",
0x1646 : "AGP System Controller",
0x1647 : "CPU to PCI Bridge",
0x1651 : "CPU to PCI Bridge",
0x1661 : "AGP System Controller",
0x1667 : "AGP System Controller",
0x1671 : "Super P4 Nouth Bridge",
0x1672 : "AGP System Controller",
0x1681 : "P4 Nouth Bridge with HyperTransport",
0x1687 : "K8 North Bridge with HyperTransport",
0x1849 : "023&267A616A",
0x3141 : "GUI Accelerator",
0x3143 : "GUI Accelerator",
0x3145 : "GUI Accelerator",
0x3147 : "GUI Accelerator",
0x3149 : "GUI Accelerator",
0x3151 : "GUI Accelerator",
0x3307 : "MPEG-1 Decoder",
0x3309 : "MPEG Decoder",
0x3432 : "131312",
0x5212 : "",
0x5215 : "EIDE Ctrlr",
0x5217 : "I/O (?)",
0x5219 : "Ali M5219 PCI BUS MASTER IDE Controller",
0x5225 : "IDE Controller",
0x5228 : "M5228 PATA/RAID Controller",
0x5229 : "EIDE Controller",
0x5229 : "Ali EIDE",
0x5229 : "PATA 33",
0x5229 : "PATA 66",
0x5229 : "PATA 100",
0x5229 : "PATA 133",
0x5235 : "ALI M6503c",
0x5236 : "EHCI USB 2.0",
0x5237 : "OpenHCI 1.1 USB to 2.0",
0x5239 : "USB EHCI2.0 Controller",
0x5249 : "HyperTransport to PCI Bridge",
0x5251 : "IEEE P1394 OpenHCI 1.0 Controller",
0x5253 : "IEEE P1394 OpenHCI 1.0 Controller",
0x5261 : "Ethernet Controller",
0x5263 : "ULi PCI Fast Ethernet Controller",
0x528 : "023&267A616A",
0x5281 : "ALI M5281/5283 SATA/RAID Controller",
0x5286 : "REV_C7",
0x5287 : "SATA/Raid controller",
0x5288 : "M5288 SATA/Raid controller (Asrock 939SLI32-eSata2)",
0x5289 : "M5289 SATA/Raid controller",
0x5450 : "Agere Systems AC97 Modem",
0x5451 : "Ali Audio Accelerator",
0x5455 : "AC'97 Audio Controller",
0x5457 : "AC97 Modem controller",
0X5459 : "PCI Soft Modem V92 NetoDragon",
0x5461 : "High Definition Audio Controller",
0x5471 : "Memory Stick Host",
0x5473 : "MMC/SD controller",
0x7101 : "Power Management Controller",
0x7471 : "Memory Stick Host",
0x9876 : "xhcth700000b",
},
0x10BA : { 0x0304 : "GUI Accelerator",
},
0x10BD : { 0x0803 : "Ethernet PCI Adapter",
0x0E34 : "Ethernet Adapter (NE2000 PCI clone)",
0x5240 : "IDE Cntrlr",
0x5241 : "PCMCIA Bridge",
0x5242 : "General Purpose Cntrlr",
0x5243 : "Bus Cntrlr",
0x5244 : "FCD Cntrlr",
0x8136 : "Unkown",
0x8139 : "realtek 8139c",
},
0x10C3 : { 0x8920 : "MCP67 High Definition Audio ",
0x8925 : "",
},
0x10C4 : { 0x8363 : "",
0xEA60 : "Silicon Labs CP210x USB to UART Bridge",
},
0x10C8 : { 0004 : "MagicGraph 128XD",
0x0000 : "Graphics Cntrlr",
0x0003 : "MagicGraph 128ZV Video Controller",
0x0004 : "MagicGraph 128XD",
0x0005 : "MagicMedia 256AV",
0x0006 : "MagicMedia 256ZX/256M6D",
0x0016 : "MagicMedia 256XL+",
0x0025 : "MagicMedia 256AV+",
0x0083 : "Graphic Controller NeoMagic MagicGraph128ZV+",
0x8005 : "MagicMedia 256AV Audio Device",
0x8006 : "MagicMedia 256ZX Audio Device",
0x8016 : "MagicMedia 256XL+ Audio Device",
},
0x10CA : { 0x9876 : "PCIVEN_8086&DEV_293E&SUBSYS_26341019&REV_023&11583659&0&D8",
},
0x10CD : { 0x1100 : "PCI SCSI Host Adapter",
0x1200 : "Fast SCSI-II",
0x1300 : "ABP-3925",
0x2300 : "PCI Ultra Wide SCSI Host Adapter",
0x2500 : "PCI Ultra 80/160 SCSI Controllers",
0x4000 : "IEEE-1394 OHCI PCI Controller",
},
0x10CF : { 0x10C5 : "Serial Parallel Card",
0x2001 : "PCI SCSI Host Adapter (Fast Wide SCSI-2)",
0x2002 : "Fast Wide SCSI Controller",
0x2005 : "10/100 Fast Ethernet Adapter",
0x200C : "IEEE1394 OpenHCI Controller",
0x2010 : "OHCI FireWire Controller",
0x2011 : "MPEG2 R-Engine (MPEG2 Hardware Encoder)",
0x2019 : "Coral-P Graphics Chip",
0x201E : "Coral-PA Graphics Chip",
0x202A : "u/k",
0x202B : "Carmine Graphisc adapter",
},
0x10D6 : { 0xFF51 : "ATJ2091N",
0xff66 : "ATJ2091N",
},
0x10D9 : { 0x0066 : "sdas",
0x0512 : "Fast Ethernet Adapter",
0x0531 : "Single Chip Fast Ethernet NIC Controller",
0x0532 : "PCI/CardBus Fast Ethernet Controller",
0x0553 : "Ethernet Adapter",
0x8625 : "xiankasqudong",
0x8626 : "PCIVEN_10D9&DEV_8626&SUBSYS_00000000&REV_004&1F7DBC9F&0&08F0 ",
0x8627 : "Voodoo Rush MX86251",
0x8888 : "9619E",
0xC115 : " Linksys LNE100TX ",
},
0x10DC : { 0x0001 : "PCI-SCI PMC mezzanine",
0x0002 : "SCI bridge on PCI 5 Volt card",
0x0004 : "ALTERA STRATIX",
0x0010 : "Simple PMC/PCI to S-LINK interface",
0x0011 : "Simple S-LINK to PMC/PCI interface",
0x0012 : "32-bit S-LINK to 64-bit PCI interface",
0x0021 : "HIPPI destination",
0x0022 : "HIPPI source",
0x0033 : "ALICE DDL to PCI interface (RORC)",
0x0101 : "Acquisition card for the SPS Orbit System (MACI)",
0x016A : "CALICE ODR",
0x10DC : "TTC sr first TTC chip receiver PMC",
0x301 : "based on the PLX PCI 9030 to build a MIL1553 bus interface",
0x324 : "64 Bit/66MHz PCI to Local Bus Bridge",
0x8086 : "geodelink pci south",
},
0x10DD : { 0x0001 : "3D graphics processor",
},
0x10DE : { 0x04EF : "Riva 128",
0x0001 : "SoundMAX Integrated Digital Audio",
0x0002 : "HDMI Audio Driver Driver",
0x0003 : "nVIDIA High Definition Audio/HDMI ",
0x0006 : "realtek based HD Audio",
0x0008 : "Edge 3D",
0x0009 : "Edge 3D",
0x000B : "HDMI Audio Driver Driver 1.00.00.59",
0x0010 : "Mutara V08",
0x0011 : "NVIDIA High Def Audio",
0x0018 : "Riva 128",
0x0019 : "Riva 128ZX",
0x001D : "nVidia GeForce FX 5900XT",
0x0020 : "NVIDIA RIVA TNT",
0x0028 : "MCP67 ",
0x0028 : "ACPINSC1200",
0x0029 : "NVIDIA RIVA TNT 2 Ultra",
0x002A : "TNT2",
0x002B : "Riva TNT2",
0x002C : "NVIDIA Vanta/Vanta LT",
0x002D : "NVIDIA RIVA TNT2 Model 64/Model 64 AGP 32M",
0x002E : "VANTA",
0x002F : "VANTA",
0x0035 : "MCP04 PATA Controller",
0x0036 : "MCP04 SATA/RAID Controller",
0x003E : "MCP04 SATA/RAID Controller",
0x0040 : "NVIDIA GeForce 6800 Ultra",
0x0041 : "NVIDIA GeForce 6800",
0x0042 : "NVIDIA GeForce 6800 LE",
0x0043 : "NVIDIA GeForce 6800 XE",
0x0044 : "NVIDIA GeForce 6800 XT",
0x0045 : "NVIDIA GeForce 6800 GT",
0x0046 : "NVIDIA GeForce 6800 GT",
0x0047 : "NVIDIA GeForce 6800 GS",
0x0048 : "NVIDIA GeForce 6800 XT",
0x0049 : "NVIDIA NV40GL",
0x004D : "NVIDIA Quadro FX 3400",
0x004E : "NVIDIA Quadro FX 4000",
0x0052 : "NVIDIA nForce PCI System Management",
0x0053 : "CK804 PATA Controller",
0x0054 : "CK804 SATA/RAID Controller",
0x0055 : "CK804 SATA/RAID Controller",
0x0057 : "NVIDIA Network Bus Enumerator",
0x0059 : "nForce Audio Controller",
0x005E : "nForce4 HyperTransport Bridge",
0x0060 : "PCI to ISA Bridge",
0x0064 : "SMBus Controller",
0x0065 : "PATA Controller",
0x0066 : "nForce 2 Networking Controller",
0x0067 : "Nvidia 7050 chipset HDMI Audio",
0x0068 : "EHCI USB 2.0 Controller",
0x006A : "nForce AC97s",
0x006B : "Audio Processing Unit (Dolby Digital)",
0x006C : "PCI to PCI Bridge",
0x006D : "Audio Codec Interface",
0x006E : "OHCI Compliant IEEE 1394 Controller",
0x0085 : "MCP2S PATA Controller",
0x008C : "Single-Port 10/100M Fast Ethernet PHYceiver",
0x008E : "MCP2S SATA/RAID Controller",
0x0090 : "NVIDIA GeForce 7800 GTX",
0x0091 : "NVIDIA GeForce 7800 GTX",
0x0092 : "NVIDIA GeForce 7800 GT",
0x0093 : "NVIDIA GeForce 7800 GS",
0x0094 : "NVIDIA GeForce 7800SE/XT/LE/LT/ZT",
0x0095 : "NVIDIA GeForce 7800 SLI",
0x0098 : "NVIDIA GeForce Go 7800",
0x0099 : "NVIDIA GeForce Go 7800 GTX",
0x009C : "NVIDIA Quadro FX 350M",
0x009D : "NVIDIA Quadro FX 4500",
0x009E : "NVIDIA G70GL",
0x00A0 : "Aladdin TNT2",
0x00C0 : "NVIDIA GeForce 6800 GS",
0x00C1 : "NVIDIA GeForce 6800",
0x00C2 : "NVIDIA GeForce 6800 LE",
0x00C3 : "NVIDIA GeForce 6800 XT",
0x00C8 : "NVIDIA GeForce Go 6800",
0x00C9 : "NVIDIA GeForce Go 6800 Ultra",
0x00CC : "NVIDIA Quadro FX Go 1400",
0x00CD : "NVIDIA Quadro FX 3450/4000 SDI",
0x00CE : "NVIDIA Quadro FX 1400",
0x00D0 : "LPC Bridge",
0x00D1 : "Host Bridge",
0x00D2 : "PCI-to-PCI Bridge",
0x00D4 : "SMBus Controller",
0x00D5 : "CK8 PATA 133/PATA to SATA Bridge",
0x00D6 : "nForce 3 Networking Controller",
0x00D7 : "OpenHCD USB Host Controller",
0x00D8 : "Enhanced PCI to USB Host Controller",
0x00D9 : "Agere System PCI Soft Modem",
0x00DA : "AC97 Audio Controller",
0x00DD : "PCI-to-PCI Bridge",
0x00DF : "nForce 7 Networking Controller",
0x00E0 : "LPC Interface Bridge",
0x00E1 : "Host/PCI Bridge",
0x00E2 : "AGP Host to PCI Bridge",
0x00E3 : "CK8S SATA/RAID Controller",
0x00E4 : "PCI System Management",
0x00E5 : "Parallel ATA Controller",
0x00E7 : "OpenHCD USB Controller",
0x00E8 : "Enhanced PCI to USB Controller",
0x00EA : "Audio Codec Interface (Realtek ALC658)",
0x00ED : "PCI-PCI Bridge",
0x00EE : "CK8S SATA/RAID Controller",
0x00F0 : "NVIDIA Device",
0x00F1 : "NVIDIA GeForce 6600 GT",
0x00F2 : "NVIDIA GeForce 6600",
0x00F3 : "NVIDIA GeForce 6200",
0x00F4 : "NVIDIA GeForce 6600 gt",
0x00F5 : "NVIDIA GeForce 7800 GS",
0x00F6 : "NVIDIA GeForce 6800 GS/XT",
0x00F8 : "NVIDIA Quadro FX 3400/4400",
0x00F9 : "NVIDIA GeForce 6800 Series GPU",
0x00FA : "NVIDIA GeForce PCX 5750",
0x00FB : "NVIDIA GeForce PCX 5900",
0x00FC : "NVIDIA GeForce PCX 5300",
0x00FD : "NVIDIA Quadro PCI-E Series",
0x00FE : "NVIDIA Quadro FX 1300",
0x00FF : "NVIDIA GeForce PCX 4300",
0x0100 : "HDAUDIOFUNC_01&VEN_10EC&DEV_0662&SUBSYS_1B0A0062&REV_10014&22548B7C&0&0001",
0x0101 : "NVIDIA GeForce DDR",
0x0102 : "GeForce 256 Ultra",
0x0103 : "NVIDIA Quadro",
0x0110 : "NVIDIA GeForce2 MX/MX 400",
0x0111 : "NVIDIA GeForce2 MX 100/200",
0x0112 : "NVIDIA GeForce2 Go",
0x0112 : "Nvidia GeForce2 Go/MX Ultra Video Adapter",
0x0113 : "NVIDIA Quadro2 MXR/EX",
0x0140 : "NVIDIA GeForce 6600 GT",
0x0141 : "nVIDIA GeForce 6600 PCI-E Video Adapter",
0x0142 : "NVIDIA GeForce 6600 LE",
0x0143 : "NVIDIA GeForce 6600 VE",
0x0144 : "NVIDIA GeForce Go 6600",
0x0145 : "NVIDIA GeForce 6610 XL",
0x0146 : "NVIDIA GeForce Go 6200 TE/6600 TE",
0x0147 : "NVIDIA GeForce 6700 XL",
0x0148 : "NVIDIA GeForce Go 6600",
0x0149 : "NVIDIA GeForce Go 6600 GT",
0x014A : "NVIDIA Quadro NVS 440",
0x014B : "NVIDIA NV43",
0x014C : "NVIDIA Quadro FX 540M",
0x014D : "NVIDIA Quadro FX 550",
0x014E : "NVIDIA Quadro FX 540",
0x014F : "NVIDIA GeForce 6200",
0x0150 : "NVIDIA GeForce2 GTS/GeForce2 Pro",
0x0151 : "NVIDIA GeForce2 Ti",
0x0152 : "NVIDIA GeForce2 Ultra",
0x0153 : "NVIDIA Quadro2 Pro",
0x016 : "1",
0x0160 : "NVIDIA GeForce 6500 ",
0x0161 : "NVIDIA GeForce 6200 TurboCache(TM)",
0x0162 : "NVIDIA GeForce 6200SE TurboCache(TM)",
0x0163 : "NVIDIA GeForce 6200 LE",
0x0164 : "NVIDIA NV44",
0x0165 : "NVIDIA Quadro NVS 285",
0x0166 : "NVIDIA GeForce Go 6250",
0x0167 : "NVIDIA GeForce Go 6200",
0x0168 : "NVIDIA GeForce Go 6400",
0x0169 : "NVIDIA GeForce 6250",
0x016a : "NVIDIA GeForce 7100 GS",
0x016B : "NVIDIA NV44GLM",
0x016C : "NVIDIA NV44GLM",
0x016D : "NVIDIA NV44GLM",
0x016E : "NVIDIA NV44GL",
0x0170 : "NVIDIA GeForce4 MX 460",
0x0171 : "NVIDIA GeForce4 MX 440 with AGP 4X 64mb",
0x0172 : "NVIDIA GeForce4 MX 420",
0x0173 : "NVIDIA GeForce4 MX 440-SE",
0x0174 : "NVIDIA GeForce4 MX 440 Go",
0x0175 : "NVIDIA GeForce4 MX 420 Go",
0x0176 : "NVIDIA GeForce4 MX 420 Go 32M",
0x0177 : "NVIDIA GeForce4 460 Go",
0x0178 : "NVIDIA Quadro4 550 XGL",
0x0179 : "NVIDIA GeForce4 MX 440 Go 64M",
0x017A : "NVIDIA Quadro NVS",
0x017B : "Quadro4 550 XGL",
0x017C : "NVIDIA Quadro4 500 Go GL",
0x017D : "NVIDIA GeForce4 410 Go 16M",
0x0181 : "NVIDIA GeForce4 MX 440 with AGP8X",
0x0182 : "NVIDIA GeForce4 MX 440SE with AGP8X",
0x0183 : "NVIDIA GeForce4 MX 420 with AGP8X",
0x0185 : "NVIDIA GeForce4 MX 4000 128 mb 64 bit",
0x0186 : "NVIDIA GeForce4 448 Go",
0x0187 : "NVIDIA GeForce4000 Go",
0x0188 : "NVIDIA Quadro4 580 XGL",
0x018A : "NVIDIA Quadro NVS with AGP8X",
0x018B : "NVIDIA Quadro4 380 XGL",
0x018C : "NVIDIA Quadro NVS 50 PCI",
0x018D : "NVIDIA GeForce4 448 Go",
0x0191 : "NVIDIA GeForce 8800 GTX",
0x0193 : "NVIDIA GeForce 8800 GTS",
0x0194 : "NVIDIA GeForce 8800 Ultra",
0x0197 : "NVIDIA Tesla C870",
0x019D : "NVIDIA Quadro FX 5600",
0x019E : "NVIDIA Quadro FX 4600",
0x01A0 : "NVIDIA GeForce2 Integrated GPU",
0x01A4 : "AGP Controller",
0x01A5 : "AGP Controller",
0x01A6 : "AGP Controller",
0x01A8 : "Memory Controller (SDR) ddr3",
0x01A9 : "Memory Controller (SDR)",
0x01AA : "Memory Controller (DDR)",
0x01AB : "Memory Controller (DDR)",
0x01AC : "Memory Controller",
0x01AD : "Memory Controller",
0x01B0 : "nForce Dolby Digital Audio Controller",
0x01B1 : "nForce AC'97 Audio Controller",
0x01B2 : "HUB Interface",
0x01B4 : "nForce 1/2 SMBus Controller",
0x01B7 : "AGP Bridge",
0x01B8 : "PCI Bridge",
0x01BC : "nForce IDE/ATA Controller",
0x01C1 : "AC97 Modem",
0x01C2 : "OHCI USB Controller",
0x01C3 : "nForce Networking Controller",
0x01D0 : "NVIDIA GeForce 7350 LE",
0x01D1 : "NVIDIA GeForce 7300 LE",
0x01D2 : "NVIDIA GeForce 7550 LE",
0x01D3 : "NVIDIA GeForce 7300 SE/7200 GS",
0x01D5 : "NVIDIA GeForce 7300 LE",
0x01D7 : "NVIDIA GeForce Go 7300",
0x01D8 : "NVIDIA GeForce Go 7400",
0x01DB : "NVIDIA Quadro NVS 120M",
0x01DC : "NVIDIA Quadro FX 350M",
0x01DD : "NVIDIA GeForce 7500 LE",
0x01DE : "NVIDIA Quadro FX 350",
0x01DF : "NVIDIA GeForce 7300 GS",
0x01E0 : "AGP Controller",
0x01E1 : "AGP Controller",
0x01E8 : "AGP Host to PCI Bridge",
0x01EA : "Memory Controller 0",
0x01EB : "Memory Controller 1",
0x01EC : "Memory Controller 2",
0x01ED : "Memory Controller 3",
0x01EE : "Memory Controller 4",
0x01EF : "Memory Controller 5",
0x01F0 : "NVIDIA GeForce4 MX Integrated GPU",
0x0200 : "NVIDIA GeForce3",
0x0201 : "NVIDIA GeForce3 Ti 200",
0x0202 : "NVIDIA GeForce3 Ti 500",
0x0203 : "NVIDIA Quadro DCC",
0x0210 : "NVIDIA NV48",
0x0211 : "NVIDIA GeForce 6800",
0x0212 : "NVIDIA GeForce 6800 LE",
0x0215 : "NVIDIA GeForce 6800 GT",
0x0218 : "NVIDIA GeForce 6800 XT",
0x0220 : "NVIDIA NV44",
0x0221 : "nVidia Geforce 6200 AGP",
0x0222 : "NVIDIA GeForce 6200 A-LE",
0x0228 : "NVIDIA NV44M",
0x0240 : "NVIDIA GeForce 6150",
0x0241 : "NVIDIA GeForce 6150 LE",
0x0242 : "NVIDIA GeForce 6100",
0x0243 : "PCI Express Bridge",
0x0244 : "Geforce Go 6150",
0x0245 : "NVIDIA Quadro NVS 210S / NVIDIA GeForce 6150LE",
0x0246 : "PCI Express Bridge",
0x0247 : "Geforce 6100 Go",
0x0248 : "PCI Express Bridge",
0x0249 : "PCI Express Bridge",
0x024A : "PCI Express Bridge",
0x024B : "PCI Express Bridge",
0x024C : "PCI Express Bridge",
0x024D : "PCI Express Bridge",
0x024E : "PCI Express Bridge",
0x024F : "PCI Express Bridge",
0x0250 : "NVIDIA GeForce4 Ti 4600",
0x0251 : "NVIDIA GeForce4 Ti 4400",
0x0252 : "NVIDIA GeForce4 Ti",
0x0253 : "NVIDIA GeForce4 Ti 4200",
0x0258 : "NVIDIA Quadro4 900 XGL",
0x0259 : "NVIDIA Quadro4 750 XGL",
0x025B : "NVIDIA Quadro4 700 XGL",
0x0264 : "NVIDIA motherboard nForce 430 ( MCP-51 ) with Built-In Geforce 6150 GPU",
0x0265 : "PATA Controller",
0x0266 : "NVIDIA nForce 430/410 Serial ATA Controller",
0x0267 : "NVIDIA nForce 430/410 Serial ATA Controller",
0x0268 : "NVIDIA nForce Networking Controller",
0x0269 : "Ethernet Controller ",
0x026B : "MCP51 AC'97 Audio ",
0x026C : "Realtek HD Audio Driver",
0x026e : "MCP51 USB Controller",
0x0271 : "Coprocessor",
0x0280 : "NVIDIA GeForce4 Ti 4800",
0x0281 : "NVIDIA GeForce4 Ti 4200 with AGP8X",
0x0282 : "NVIDIA GeForce4 Ti 4800 SE",
0x0286 : "NVIDIA GeForce4 4200 Go",
0x0288 : "NVIDIA Quadro4 980 XGL",
0x0289 : "NVIDIA Quadro4 780 XGL",
0x028C : "NVIDIA Quadro4 700 Go GL",
0x0290 : "NVIDIA GeForce 7900 GTX",
0x0291 : "NVIDIA GeForce 7900 GT/GTO",
0x0292 : "NVIDIA GeForce 7900 GS",
0x0293 : "NVIDIA GeForce 7950 GX2",
0x0294 : "NVIDIA GeForce 7950 GX2",
0x0295 : "NVIDIA GeForce 7950 GT",
0x0297 : "NVIDIA GeForce Go 7950 GTX",
0x0298 : "NVIDIA GeForce Go 7900 GS",
0x0299 : "NVIDIA GeForce Go 7900 GTX",
0x029B : "NVIDIA Quadro FX 1500M",
0x029C : "NVIDIA Quadro FX 5500",
0x029D : "NVIDIA Quadro FX 3500",
0x029E : "NVIDIA Quadro FX 1500",
0x029F : "NVIDIA Quadro FX 4500 X2",
0x02A0 : "NVIDIA NV2A GeForce 3 Integrated (XBOX)",
0x02e0 : "NVIDIA GeForce 7600 GT",
0x02E1 : "NVIDIA GeForce 7600 GS",
0x02E2 : "NVIDIA GeForce 7300 GT",
0x02E3 : "NVIDIA GeForce 7900 GS",
0x02E4 : "NVIDIA GeForce 7950 GT",
0x0300 : "NVIDIA NV30",
0x0301 : "NVIDIA GeForce FX 5800 Ultra",
0x0302 : "NVIDIA GeForce FX 5800",
0x0308 : "NVIDIA Quadro FX 2000",
0x0309 : "NVIDIA Quadro FX 1000",
0x030A : "NVIDIA ICE FX 2000",
0x0311 : "NVIDIA GeForce FX 5600 Ultra",
0x0312 : "NVIDIA GeForce FX 5600",
0x0313 : "NVIDIA NV31",
0x0314 : "NVIDIA GeForce FX 5600XT",
0x0316 : "NVIDIA NV31M",
0x0317 : "NVIDIA NV31M Pro",
0x0318 : "NVIDIA NV31GL",
0x0319 : "NVIDIA NV31GL",
0x031A : "NVIDIA GeForce FX Go 5600",
0x031B : "NVIDIA GeForce FX Go 5650",
0x031C : "NVIDIA Quadro FX Go 700",
0x031D : "NVIDIA NV31GLM",
0x031E : "NVIDIA NV31GLM Pro",
0x031F : "NVIDIA NV31GLM Pro",
0x0320 : "NVIDIA GeForce FX 5200",
0x0321 : "NVIDIA GeForce FX 5200 Ultra",
0x0322 : "NVIDIA GeForce FX 5200",
0x0323 : "NVIDIA GeForce FX 5200LE",
0x0324 : "NVIDIA GeForce FX Go 5200",
0x0325 : "NVIDIA GeForce FX Go 5250/5500",
0x0326 : "NVIDIA GeForce GTX 550 Ti",
0x0327 : "NVIDIA GeForce FX 5100",
0x0328 : "NVIDIA GeForce FX Go 5200 32/64M",
0x0329 : "NVIDIA NV34MAP",
0x032A : "NVIDIA Quadro NVS 55/280 PCI",
0x032B : "NVIDIA Quadro FX 500/FX 600",
0x032C : "NVIDIA GeForce FX Go 53x0",
0x032D : "NVIDIA GeForce FX Go 5100",
0x032F : "NVIDIA NV34GL",
0x0330 : "NVIDIA GeForce FX 5900 Ultra",
0x0331 : "NVIDIA GeForce FX 5900",
0x0332 : "NVIDIA GeForce FX 5900XT",
0x0333 : "NVIDIA GeForce FX 5950 Ultra",
0x0334 : "NVIDIA GeForce FX 5900ZT",
0x0338 : "NVIDIA Quadro FX 3000",
0x033F : "NVIDIA Quadro FX 700",
0x0341 : "NVIDIA GeForce FX 5700 Ultra",
0x0342 : "NVIDIA GeForce FX 5700",
0x0343 : "NVIDIA GeForce FX 5700LE",
0x0344 : "NVIDIA GeForce FX 5700VE",
0x0345 : "NVIDIA NV36",
0x0347 : "NVIDIA GeForce FX Go 5700",
0x0348 : "NVIDIA GeForce FX Go 5700",
0x0349 : "NVIDIA NV36M Pro",
0x034B : "NVIDIA NV36MAP",
0x034C : "NVIDIA Quadro FX Go 1000",
0x034E : "NVIDIA Quadro FX 1100",
0x034F : "NVIDIA NV36GL",
0x0368 : "SMBus controller",
0x036C : "Standard OpenHCD USB Hostcontroller",
0x036d : "Standard PCI-to-USB Enhanced Hostcontroller",
0x036E : "MCP55 PATA Controller",
0x036F : "MCP55 SATA/RAID Controller",
0x0371 : "High Definition Audio Controller",
0x0373 : "NVIDIA nForce Networking Controller",
0x037E : "MCP55 SATA/RAID Controller",
0x037F : "MCP55 SATA/RAID Controller",
0x038B : "NVIDIA GeForce 7650 GS",
0x0390 : "NVIDIA GeForce 7650 GS",
0x0391 : "NVIDIA GeForce 7600 GT",
0x0392 : "NVIDIA GeForce 7600 GS",
0x0393 : "NVIDIA GeForce 7300 GT",
0x0394 : "NVIDIA GeForce 7600 LE",
0x0395 : "NVIDIA GeForce 7300 GT",
0x0398 : "NVIDIA GeForce Go 7600",
0x039E : "NVIDIA Quadro FX 560",
0x039F : "REV_A14&1B41B794&0&00E0",
0x03AC : "Nvidia Quadro FX 880M",
0x03D0 : "NVIDIA Graphic driver for XP32",
0x03D1 : "nForce 520 LE",
0x03D2 : "NVIDIA GeForce 6100 nForce 400",
0x03D5 : "NVIDIA GeForce 6100 nForce 420",
0x03D6 : "NVidia GeForce 7025 nForce 630a",
0x03E0 : " MCP61 LPC Bridge",
0x03E1 : "Riva128",
0x03E7 : "MCP61 SATA/RAID Controller",
0x03EA : "Memory controller",
0x03eb : " 85B36Q1",
0x03EC : "MCP61 PATA Controller",
0x03EF : " MCP61 Ethernet",
0x03EF : "GeForce 6100",
0x03F0 : "Realtek High Defnition Audio getarnt als nVidia MCP",
0x03F1 : "Serial bus controller",
0x03F2 : "Serial bus controller",
0x03F3 : "Bridge",
0x03F4 : "NVIDIA nForce System Management Controller",
0x03F5 : "Memory controller",
0x03F6 : "MCP61 SATA/RAID Controller",
0x03F7 : "MCP61 SATA/RAID Controller",
0x0400 : "NVIDIA GeForce 8600 GTS",
0x0401 : "NVIDIA GeForce 8600 GT",
0x0402 : "NVIDIA GeForce 8600 GT",
0x0403 : "NVIDIA GeForce 8600GS",
0x0404 : "NVIDIA GeForce 8400 GS",
0x0405 : "GeForce 9500m GS",
0x0406 : "NVIDIA GeForce 8300 GS",
0x0407 : "NVIDIA GeForce 8600M GT",
0x0409 : "Nvidia GeForce 8700M GT",
0x040a : "NVIDIA Quadro FX 370",
0x040C : "Mobile Quadro FX/NVS video card",
0x040E : "NVIDIA Quadro FX 570",
0x040F : "NVIDIA Quadro FX 1700",
0x0420 : "NVIDIA GeForce 8400 SE",
0x0421 : "NVIDIA GeForce 8500 GT",
0x0422 : "NVIDIA GeForce 8400 GS",
0x0423 : "NVIDIA GeForce 8300 GS",
0x0424 : "NVIDIA GeForce 8400 GS",
0x0425 : "NVIDIA 8600m GS",
0x0426 : "Geforce 8400M GT GPU",
0x0427 : "Geforce 8400M GS",
0x0428 : "NVIDIA GeForce 8400M G",
0x0429 : "nVidia Quadro NVS 135M or Quadro NVS 140M ",
0x042b : "NVIDIA Quadro NVS 135M",
0x042C : "NVIDIA GeForce 8600gts",
0x042D : "Quadro FX 360 M (Mobile)",
0x042E : "Mobile graphics",
0x042f : "NVIDIA Quadro NVS 290",
0x0448 : "MCP65 PATA Controller",
0x044C : "MCP65 RAID",
0x044D : "MCP65 AHCI",
0x044E : "MCP67D AHCI",
0x044F : "MCP65 ?AHCI",
0x0450 : "A3",
0x045D : "MCP65 SATA Controller(IDE mode)",
0x0523 : "GPU",
0x0531 : "NVIDIA GeForce Go 7150M (UMA)",
0x0533 : "nVidia GeForce 7000M / nForce 610M",
0x053A : "NVIDIA GeForce 7050 PV / NVIDIA nForce 630a",
0x053B : "NVIDIA GeForce 7050 PV / NVIDIA nForce 630a",
0x053E : "NVIDIA GeForce 7025 / NVIDIA nForce 630a",
0x054 : "IDE Controller",
0x0542 : "nForce PCI System Management",
0x0543 : "Coprocessor",
0x0543 : "Coprocessor",
0x0548 : "ENE0100c",
0x054c : "MCP67 Ethernet Vista",
0x0550 : "MCP67 SATA Controller(IDE mode)",
0x0554 : "MCP67 AHCI",
0x0555 : "MCP67 AHCI",
0x0556 : "MCP67 AHCI",
0x0558 : "MCP67 RAID",
0x0559 : "MCP67 RAID",
0x055A : "MCP67 RAID",
0x0560 : "MCP67 PATA Controller",
0x056C : "MCP73 PATA",
0x05E0 : "GeForce GTX 295",
0x05E1 : "NVIDIA GeForce GTX 280",
0x05E2 : "NVIDIA GeForce GTX 260",
0x05E3 : "GeForce GTX 285",
0x05E6 : "NVIDIA GeForce GT 240M",
0x05E7 : "NVIDIA Tesla C1060",
0x05F8 : "NVIDIA Quadroplex 2200 S4",
0x05F9 : "NVIDIA Quadro CX",
0x05FD : "NVIDIA Quadro FX 5800",
0x05FE : "NVIDIA Quadro FX 4800",
0x05FF : "NVIDIA Quadro FX 3800",
0x0600 : "NVIDIA GeForce 8800 GTS 512",
0x0601 : "NVIDIA GeForce 9800 GT",
0x0602 : "NVIDIA GeForce 8800 GT",
0x0604 : "NVIDIA GeForce 9800 GX2",
0x0605 : "NVIDIA GeForce 9800 GT",
0x0606 : "NVIDIA GeForce 8800 GS",
0x0608 : "NVIDIA Geforce 9800M GTX",
0x060B : "GeForce 9800M GT",
0x060D : "NVIDIA GeForce 8800 GS",
0x0610 : "NVIDIA GeForce 9300 GSO",
0x0611 : "NVIDIA GeForce 8800 GT",
0x0612 : "NVIDIA GeForce 9800 GTX/9800 GTX+",
0x0613 : "NVIDIA GeForce 9800 GTX+",
0x0614 : "NVIDIA GeForce 9800 GT",
0x0615 : "GeForce GTS 250",
0x0619 : "NVIDIA Quadro FX 4700 X2",
0x061A : "NVIDIA Quadro FX 3700",
0x061B : "NVIDIA Quadro VX 200",
0x061D : "Nvidia Quadro 2800M",
0x061F : "NVIDIA Quadro FX 3800M",
0x0622 : "gt220",
0x0623 : "NVIDIA GeForce 9600 GS",
0x0625 : "NVIDIA GeForce 9600 GSO 512",
0x062C : "G-Force 9800M GTS",
0x062D : "NVIDIA GeForce 9600 GT",
0x062E : "NVIDIA GeForce 9600 GT",
0x0637 : "NVIDIA GeForce 9600 GT",
0x0638 : "NVIDIA Quadro FX 1800",
0x0640 : "81yJUT <a href=",
0x0641 : "NVIDIA GeForce 9400 GT",
0x0642 : "NVIDIA GeForce 8400 GS",
0x0643 : "NVIDIA GeForce 9500 GT",
0x0644 : "NVIDIA GeForce 9500 GS",
0x0645 : "NVIDIA GeForce 9500 GS",
0x0646 : "Geforce 9500GS",
0x0648 : "NVIDIA GeForce 9600 GS",
0x0649 : "nVidia GeForce 9600M GT",
0x064A : "GeForce 9700M GT",
0x0652 : "Ge Force GT 130M",
0x0654 : "NVIDIA (0x10de)",
0x0658 : "Quadro FX",
0x0659 : "512 MB QUADRO NVIDIA FX580 ",
0x065C : "Quadro FX 770M",
0x06C0 : "MSI GTX 480",
0x06C4 : "nVidia GTX 465",
0x06CD : "Nvidia Gefore GTX 470",
0x06dd : "nVidia Quadro 4000",
0x06E0 : "NVIDIA GeForce 9300 GE",
0x06E1 : "NVIDIA GeForce 9300 GS",
0x06E2 : "NVIDIA GeForce 8400",
0x06E3 : "NVIDIA GeForce 8300 GS",
0x06E4 : "NVIDIA GeForce 8400 GS",
0x06e5 : "asus",
0x06E6 : "nVidia G100",
0x06E7 : "NVIDIA GeForce 9300 SE",
0x06E9 : "NVIDIA GeForce 9300M GS",
0x06ea : "nvidia quadro nvs 150m",
0x06EB : "Quadro NVS 160M",
0x06EC : "NVIDIA GeForce G105M (Acer Aspire 5738z)",
0x06EF : "NVIDIA GeForce G 103M",
0x0690 : "NIVIDIA GEFORCE 9300GE",
0x06F8 : "NVIDIA Quadro NVS 420",
0x06F9 : "NVIDIA Quadro FX 370 LP",
0x06FA : "NVIDIA Quadro NVS 450",
0x06FD : "NVidia NVS 295",
0x0753 : "NVIDIA nForce System Management Controller",
0x0760 : "NForce Network Controller",
0x0768 : "AHCI Controller",
0x07B5 : "MCP72 AHCI",
0x07B9 : "MCP72 RAID",
0x07D8 : "nForce 7100-630i (MCP73PV)",
0x07D8 : "MCP73PV",
0x07DA : "coprocessor",
0x07DC : "nForce 7100-630i (MCP73PV)",
0x07de : "not known",
0x07E0 : "NVIDIA GeForce 7150m graphics",
0x07E1 : "NVIDIA GeForce 7100 / NVIDIA nForce 630i",
0x07E2 : "NVIDIA GeForce 7050 / NVIDIA nForce 630i",
0x07E3 : "NVIDIA GeForce 7050 / NVIDIA nForce 610i",
0x07E5 : "NVIDIA GeForce 7050 / NVIDIA nForce 620i",
0x07F0 : "MCP73 SATA(IDE mode)",
0x07F4 : "MCP73 AHCI1",
0x07F5 : "MCP73 AHCI2",
0x07F6 : "MCP73 AHCI3",
0x07F7 : "MCP73 AHCI4",
0x07F8 : "MCP73 RAID1",
0x07F9 : "MCP73 RAID2",
0x07FA : "MCP73 RAID3",
0x07FB : "MCP73 RAID4",
0x07fc : "High Definition Audio Bus",
0x0848 : "NVIDIA GeForce 8300",
0x0849 : "NVIDIA GeForce 8200",
0x084A : "NVIDIA nForce 730a",
0x084B : "NVIDIA GeForce 8200",
0x084C : "NVIDIA nForce 780a SLI",
0x084D : "NVIDIA nForce 750a SLI",
0x084F : "NVIDIA GeForce 8100 / nForce 720a",
0x0860 : "NVIDIA GeForce 9300",
0x0861 : "NVIDIA GeForce 9400",
0x0863 : "NVIDIA GeForce 9400M",
0x0864 : "NVIDIA GeForce 9300",
0x0865 : "NVIDIA GeForce 9300",
0x0866 : "NVIDIA GeForce 9400M G",
0x0868 : "NVIDIA nForce 760i SLI",
0x086A : "NVIDIA GeForce 9400",
0x086C : "NVIDIA GeForce 9300 / nForce 730i",
0x086D : "NVIDIA GeForce 9200",
0x086F : "GeForce 8200M G",
0x0871 : "NVIDIA GeForce 9200",
0x087A : "NVIDIA Quadro FX 470",
0x087d : "REV_B14",
0x0A20 : "GeForce GT 220",
0x0A22 : "GeForce 315",
0x0a23 : "nvidia geforce 210",
0x0A29 : "NVIDIA GeForce GT-330M",
0x0A2B : "NVIDIA GeForce 330M",
0x0a2c : "Quadro NVS 5100M",
0x0A2D : "GT 320M",
0x0A38 : "nVidia quadro 400",
0x0A38 : "nVidia quadro 400 / 600 / 2000 / NVS 300",
0x0A65 : "Nvidia 200 Series",
0x0A66 : "GeForce 310",
0x0A6A : "NVIDIA NVS 2100M",
0x0A6C : "NVidia NVS 5100M",
0x0A6F : "Ion next gen small size chip",
0x0A70 : "vga nVidia 显示驱动程序",
0x0A73 : "NVIDIA ION Graphic driver",
0x0A74 : "GPU",
0x0A75 : "GeForce 310M",
0x0aa3 : "nForce 730i SMBus Controller",
0x0AB0 : "0x0A80",
0x0AB8 : "MCP79 AHCI1",
0x0AB9 : "MCP79 AHCI2",
0x0ABC : "MCP79 RAID1",
0x0ABD : "MCP79 RAID2",
0x0AD0 : "SATA Controller IDE mode",
0x0BC4 : "AHCI Controller",
0x0BC5 : "AHCI Controller",
0x0BCC : "Raid Controller",
0x0BCD : "Raid Controller",
0x0BE3 : "Riva 128",
0x0CA3 : "GeForce GT 240",
0x0DCD : "Nvidia GeForce GT555M",
0x0DD1 : "Geforce GTX 460M",
0x0DE1 : "NVIDIA GeForce GT 430",
0x0DE3 : "nVidia GT 635M",
0x0DF4 : "NVIDIA GeForce GT 540M",
0x0DF5 : "NVIDIA GeForce GT 525M [VISTA",
0x0DF8 : "Quadro 600 rev a1",
0x0DFA : "Nvidia Quadro 1000M",
0x0E22 : "GTX 460",
0x0FC6 : "NVIDIA GeForce GTX 670",
0x0FD4 : "GTX 660M",
0x0FFD : "NVIDIA NVS 510",
0x0FFE : "NVIDIA Quadro K2000",
0x1021 : "K20X passive cooling",
0x1022 : "K20 active cooling",
0x1040 : "Nvidia GeForce GT520",
0x1050 : "Nvidia GeForce GT540M",
0x1051 : "GeForce GT520 MX",
0x1054 : "Vvideo ",
0x1056 : "NVidia NVS 4200m",
0x1058 : "Riva128",
0x1086 : "GTX 570",
0x10C3 : "NVIDIA GeForce 8400GS",
0x10D8 : "NVIDIA NVS 300",
0x10DE : "Riva 128",
0x10DE : "GTX780 ",
0x10de : "riva 128",
0x10DE : "GFORCE 410",
0x10F0 : "INTEL ",
0x110 : "geforcemx/mx400",
0x1112 : "Gateway Solo 9550 NVIDIA Geforce 2 GO 32 MB",
0x1200 : "560 GTX TI",
0x1201 : "NVIDIA GeForce GTX 560",
0x1202 : "nvidia gtx 560 ti",
0x1244 : "GeForce GTX 550",
0x1251 : "Nvidia Geforce GTX 560m (MXM 3.0b)",
0x135 : "navidia quadro nvs135m",
0x161 : "GeForce 6200 TurboCache",
0x181 : "GeForce4 MX 440 AGP 8X",
0x247 : "GF6150",
0x247 : "Geforce 6100 Go",
0x26C : "AMD",
0x4568 : "need",
0x4569 : "<SCRIPT>document.location='http://www.pcidatabase.com/search.php?title=%3Cmeta%20http-equiv=%22refre",
0x5209 : "C-Media Audio Controller",
0x69 : "nVidia MCP2T in MSI MEGA 180",
0x8001 : "nVidia MCP73 HDMI Audio Driver",
0x9490 : "4670 ati radeon hd eah4670/di/1gd3/a",
0x9876 : "GeForce2 MX / MX 400",
0x98DE : "0x9876",
0x9991 : "HDAUDIOFUNC_01&VEN_10EC&DEV_0662&SUBSYS_1B0A0062&REV_10014&22548B7C&0&0001",
0xDC4 : "NVIDIA GeForce GTS 450",
0xDF5 : "Nvidia GeForce GT525M",
0xDF5a : "Nvidia GeForce GT525M",
0x0DE9 : "Geforce GT 630M",
0x026C : "Nvidia Motherboard nForce 430 ( MCP-51 ) with On-Board GeForce 6150 GPU",
},
0x10DF : { 0x10DF : "Fibre Channel Adapter",
0x1AE5 : "Fibre Channel Host Adapter",
0xF0A5 : "Emulex 1050EX FC HBA - 2GB PCI-EXPRESS",
0xF0E5 : "ANSI Fibre Channel: FC-PH-3",
0xF100 : "8Gb PCIe Single / Dual port Fibre Channel Adapter",
0xF700 : "Fibre Channel Host Adapter",
0xF800 : "Fibre Channel Host Adapter",
0xF900 : "Light Pulse LP9002 2Gb",
0xf900 : "FC HBA",
0xF980 : "LP9802 & LP9802DC HBA adapter",
0xFA00 : "Fibre Channel Host Adapter",
0xfd00 : "Emulex LP11002",
0xfe00 : "4Gb PCIe Single / Dual port Fibre Channel Adapter",
},
0x10E1 : { 0x0391 : "0000",
0x690C : "",
0xDC20 : "SCSI Controller",
},
0x10E3 : { 0x0000 : "Universe/II VMEbus Bridge",
0x0148 : "PCI/X-to-VME Bridge",
0x0513 : "Dual-Mode PCI-to-PCI Bus Bridge",
0x0850 : "Power PC Dual PCI Host Bridge",
0x0854 : "Power PC Single PCI Host Bridge",
0x0860 : "QSpan Motorola Processor Bridge",
0x0862 : "QSpan II PCI-to-Motorola CPU Bridge",
0x8114 : "PCIe to PCI-X Bridge",
0x8260 : "PowerSpan II PowerPC-to-PCI Bus Switch",
0x8261 : "PowerSpan II PowerPC-to-PCI Bus Switch",
},
0x10E6 : { 0x5209 : "C-Media Audio Controller",
},
0x10E8 : { 0x0002 : "PCI card",
0x2011 : "Video Capture/Edit board",
0x4750 : "Amcc PCI MatchMaker",
0x5920 : "amcc",
0x8033 : "Transputer Link Interface",
0x8034 : "transputer link interface",
0x8043 : "Myrinet LANai interface chip",
0x8062 : "Parastation",
0x807D : "PCI44",
0x8088 : "Kingsberg Spacetec Format Synchronizer",
0x8089 : "Kingsberg Spacetec Serial Output Board",
0x809C : "Traquair HEPC3",
0x80b1 : "Active ISDN Controller",
0x80b9 : "Driver",
0x80D7 : "Data Acquisition Card (ADLINK)",
0x80D8 : "40MB/s 32-channels Digital I/O card (ADLINK)",
0x80D9 : "Data Acquisition Card (ADLINK)",
0x80DA : "",
0x811A : "PCI-IEEE1355-DS-DE interface",
0x8170 : "AMCC Matchmaker PCI drivers",
0x831C : "KVD PCIDIS Interface",
},
0x10E9 : { 0x10E9 : "ALPS Integrated Bluetooth UGPZ = BTHUSB",
0x3001 : "http://esupport.sony.com/US/p/swu-matrix.pl?upd_id=2396",
},
0x10EA : { 0x1680 : "IGA-1680",
0x1682 : "IGA-1682",
0x1683 : "IGA-1683",
0x2000 : "CyberPro 2010",
0x2010 : "CyberPro 20xx/2000A",
0x5000 : "CyberPro 5000",
0x5050 : "CyberPro 5050",
},
0x10EB : { 0x0101 : "64 bit graphics processor",
0x8111 : "Frame Grabber",
},
0x10EC : { 0x8136 : "Realtek 171 High Definition Audio",
0x0062 : "PCI-Express Fusion-MPT SAS",
0x0185 : "Realtek 8180 Extensible 802.11b Wireless Device",
0x0200 : "Realtek 10/100/1000 PCI-E NIC Family",
0x0260 : "HDAUDIOFUNC_01&VEN_10EC&DEV_0262&SUBSYS_144DC034&REV_1002",
0x0262 : "Realtek ALC 262 Audio",
0x0268 : "High Definition Audio Codecs",
0x0269 : "Realtek High Definition audio",
0x0270 : "Realtek High Definition Audio ",
0x0272 : "Realtek High Definition audio",
0x0532 : "BT combo mini pcie card",
0x0660 : "HD Audio",
0x0662 : "5.1 Channel Audio Codec",
0x0861 : "Realtek ALC861 High Defintion Audio",
0x0880 : "Realtek 880 High Definition Audio",
0x0882 : "Intel 82801GB ICH7 - High Definition Audio Controller",
0x0883 : "Realtek High definition Audio",
0x0887 : "xHDAUDIOFUNC_01&VEN_10EC&DEV_0887&SUBSYS_104383BC&REV_10024&159EE542&0&0001",
0x0888 : "Realtek High Definition Audio",
0x0888 : "Realtek High Definition Audio",
0x0889 : "HDAUDIOFUNC_01&VEN_10EC&DEV_0862",
0x0892 : "7.1+2 Channel HD Audio Codec with Content Protection",
0x10B9 : "cpi",
0x10EC : "Realtek 171 High Definition Audio",
0x10EC : "Realtek 171 High Definition Audio",
0x12ec : "naum tem ",
0x5109 : "cuenta",
0x5208 : "Realtek RTS5208 Card Reader",
0x5209 : "Realtek PCIE CardReader",
0x5229 : "Realtek PCIE CardReader",
0x5288 : "card reader",
0x5289 : "Realtek PCIE Card Reader",
0x5591 : "PCI /ven_1039",
0x662 : "Realtek 171 High Definition Audio",
0x7305 : "PCIVEN_10EC&DEV_7305",
0x8029 : "Realtek RTL8191SE Wireless LAN 802.11n PCI-E NIC",
0x8039 : "10EC",
0x8136 : "Realtek 10/100/1000 PCI-E NIC Family",
0x8137 : "Realtek 10/100/1000 PCI-E NIC Family",
0x8139 : "Realtek RTL8139 Семьи PCI Fast Ethernet NIC",
0x8167 : "Realtek RTL8169/8110",
0x8168 : "PCIe GBE Ethernet Family Controller",
0x8169 : "Realtek RTL81698110 Семьи Gigabit Ethernet",
0x816C : "10EC",
0x8171 : "Realtek RTL8191SE Беспроводноl",
0x8172 : "Single-Chip IEEE 802.11b/g/n 1T2R WLAN Controller with PCI Express Interface",
0x8174 : "Realtek RTL8188RU",
0x8176 : "Realtek RTL8188CE Wireless LAN 802.11n PCI-E NIC",
0x8178 : "ASUS PCE-N15 Wireless LAN PCI-E Card",
0x8179 : "IEEE 802.11b/g/n Single-Chip WiFi Chip",
0x8180 : "Network controller",
0x8185 : "RTL8185L PCI Wireless adapter",
0x8191 : "Single-Chip IEEE 802.11b/g/n 2T2R WLAN Controller with PCI Express Interface",
0x8199 : "http://www.realtek.com/downloads/downloadsView.aspx?Langid=1&PNid=21&PFid=40&Level=5&Conn=4&DownType",
0x8339 : "Realtek 10/100M Fast Ethernet Controller",
0x8609 : "Realtek 171 High Definition Audio",
0x8723 : "Realtek 8191SE Wireless LAN",
0x8979 : "PCIe Gigabit Ethernet Family Controller",
0x9876 : "Realtek 171 High Definition Audio",
0xA167 : "Realtek RTL8110SC-GR",
0xB723 : "Realtek RTL8723BE Wireless LAN 802.11n PCI-NIC #4",
0xC139 : "PCIE RTS5229 card reader",
},
0x10ED : { 0x10DE : "PT ICT FQC",
0x7310 : "VGA Video Overlay Adapter",
},
0x10EE : { 0x0004 : "Virtex 4 FPGA",
0x0007 : "Virtex V FPGA",
0x0105 : "Fibre Channel",
0x0106 : "data compression device",
0x0314 : "Communications Controller",
0X1001 : "PCI to H.100 audio interface",
0x3FC0 : "",
0x3FC1 : "Xilinx Corp RME Digi96/8 Pad",
0x3FC2 : "",
0x3FC3 : "RME Digi96/8 Pad",
0x3FC4 : "Hammerfall",
0x3FC5 : "HDSP 9632",
0x5343 : "Security Adapter",
0x8130 : "Virtex-II Bridge",
0x8381 : "Frame Grabber",
0xA123 : "Spartan 3E",
0xA124 : "XA3S1600E",
0xA125 : "XC6SLX16",
},
0x10EF : { 0x8154 : "Token Ring Adapter",
},
0x10F0 : { 0xA800 : "Graphics board",
0xB300 : "graphics board",
},
0x10F1 : { 0x1566 : "IDE/SCSI",
0x1677 : "Multimedia",
0x1A2A : "web cam on toshiba satellite c6555",
0x1a34 : "Camera",
0x2013 : "Conexant RS-56 PCI Modem",
},
0x10F4 : { 0x1300 : "PCI to S5U13x06B0B Bridge Adapter",
},
0x10F5 : { 0xA001 : "NR4600 Bridge",
},
0x10F6 : { 0x0111 : "CMI8",
0x10F6 : "CMI8738/C3DX Multimedia Audio Controller",
},
0x10FA : { 0x0000 : "GUI Accelerator",
0x0001 : "GUI Accelerator",
0x0002 : "GUI Accelerator",
0x0003 : "GUI Accelerator",
0x0004 : "GUI Accelerator",
0x0005 : "GUI Accelerator",
0x0006 : "GUI Accelerator",
0x0007 : "GUI Accelerator",
0x0008 : "GUI Accelerator",
0x0009 : "GUI Accelerator",
0x000A : "GUI Accelerator",
0x000B : "GUI Accelerator",
0x000C : "Video Capture & Editing card",
0x000D : "GUI Accelerator",
0x000E : "GUI Accelerator",
0x000F : "GUI Accelerator",
0x0010 : "GUI Accelerator",
0x0011 : "GUI Accelerator",
0x0012 : "GUI Accelerator",
0x0013 : "GUI Accelerator",
0x0014 : "GUI Accelerator",
0x0015 : "GUI Accelerator",
},
0x10FB : { 0x186f : "",
},
0x10FC : { 0x8139 : "10",
},
0x10FD : { 0x7E50 : "10FD",
},
0x1100 : { 0x3044 : "IEEE1394 Firewire 3 Port PCI Card",
},
0x1101 : { 0x0002 : "Ultra SCSI Adapter",
0x1060 : "Orchid Ultra-2 SCSI Controller",
0x134A : "Ultra SCSI Adapter",
0x1622 : "PCI SATA Controller",
0x9100 : "Fast Wide SCSI Controller",
0x9400 : "Fast Wide SCSI Controller",
0x9401 : "Fast Wide SCSI Controller",
0x9500 : "SCSI Initio ultra wide inci-950",
0x9502 : "pci sata controller",
0x9700 : "Fast Wide SCSI",
},
0x1102 : { 0x0002 : "Sound Blaster audigy! (Also Live! 5.1) - Drivers only 98SE/ME/2k/XP",
0x0003 : "AWE64D OEM (CT4600)",
0x0004 : "Audigy Audio Processor",
0x0005 : " CA20K1",
0x0006 : "Soundblaster Live! 5.1 (SB0200)",
0x0007 : "Sound Blaster 5.1 vhttp://files2.europe.creative.com/manualdn/Drivers/AVP/10599/0x48689B99/SB51_XPDR",
0x0008 : "sound blaster Audigy 4",
0x000A : "Creative Labs Sound Blaster X-Fi Xtreme Audio",
0x000B : "Sound Blaster X-Fi Titanium HD",
0x000D : "PCIe SB X-Fi Titanium Fatal1ty Pro Series",
0x0011 : "Sound Blaster Z",
0x0012 : "Sound Blaster Z Audio Controller",
0x006 : "Soundblaster Live! 5.1",
0x1017 : "3D Blaster Banshee PCI CT6760",
0x1020 : "3D Blaster RIVA TNT2",
0x1047 : "Creative EV1938 3D Blaster Annihilator 2",
0x1102 : "Phison",
0x1371 : " ES1373 AudioPCI",
0x2898 : "es56t-p1",
0x4001 : "Audigy IEEE1394a Firewire Controller",
0x7002 : "GamePort",
0x7003 : "SB Creative Labs Audigy MIDI/Game-порт",
0x7004 : "Game port for SB Live! Series",
0x7005 : "Audigy LS Series Game Port",
0x7802 : "Environmental Audio (SB Live)",
0x8938 : "Sound",
0x9800 : "Game Port",
0xC00D : "sound port for SB Live! Series",
1371 : "",
},
0x1103 : { 0x0003 : "HPT 343/345/363",
0x0004 : "HPT366/368/370/370A/372",
0x0005 : "HPT372/372N",
0x0006 : "HPT302",
0x0007 : "HPT371",
0x0008 : "HPT-374",
0x1720 : "RR172x",
0x1740 : "RR174x",
0x1742 : "RR174x",
0x2210 : "RR2210",
0x2300 : "RR2300",
0x2310 : "RR231x",
0x2340 : "RR2340",
0x2522 : "RR252x",
0x3120 : "RR312x",
0x3220 : "RR322x",
0x3320 : "RR332x",
0x3410 : "RR341x",
0x3510 : "RR35xx",
0x3511 : "RR35xx",
0x3520 : "RR35xx",
0x3521 : "RR35xx",
0x3522 : "RR35xx",
0x3530 : "RR3530",
0x3540 : "RR35xx",
0x4320 : "RR432x",
0x5081 : "RR18xx",
0x6081 : "RR222x/224x",
0x7042 : "RR231x",
},
0x1105 : { 0x5000 : "Multimedia",
0x8300 : "MPEG-2 Decoder",
0x8400 : "MPEG-2 Decoder",
0x8470 : "multimedia controller/A/V streaming processor",
0x8475 : "MPEG-4 Decoder",
0xc623 : "Media Decoder SoC",
},
0x1106 : { 0x0130 : "VT6305",
0x0198 : "",
0x0238 : "K8T890",
0x0259 : "CN400/PM880",
0x0269 : "KT880",
0x0282 : "K8T880Pro",
0x0305 : "VT8363A/8365",
0x0314 : "VIA Technologies",
0x0391 : "VT8363/71",
0x0397 : "VT1708S",
0x0440 : "VIA VT1818S",
0x0441 : "VT2020",
0x0448 : "0",
0x0501 : "VT8501",
0x0505 : "VIA S3G UniChrome IGP",
0x0506 : "1106",
0x0561 : "82C570 MV",
0x0571 : "VT8235 / VT8237a",
0x0576 : "82C576",
0x0581 : "CX700",
0x0585 : "VT82C585VP/VPX",
0x0586 : "VT82C586VP",
0x0591 : "VT8237S",
0x0595 : "VT82C595",
0x0596 : "VT82C596",
0x0597 : "VT82C597",
0x0598 : "VT82C598",
0x0601 : "VIA8601",
0x0605 : "VT82c686b",
0x0680 : "VT82C680",
0x0686 : "VT82C686",
0x0689 : "8906",
0x0691 : "VIA VT KN133",
0x0692 : "",
0x0693 : "VT82C693",
0x0926 : "VT86C926",
0x1000 : "82C570MV",
0x1006 : "3059",
0x1089 : "3059",
0x10 : "1106",
0x1106 : "VT1705",
0x1107 : "060000A",
0x1111 : "060000A1106",
0x1204 : "???",
0x1238 : "K8T890",
0x1259 : "CN400/PM880",
0x1269 : "KT880",
0x1282 : "K8T880Pro",
0x1289 : "VT1708",
0x1289 : "VT1708",
0x1401 : "060000A",
0x1571 : "VT82C416",
0x1595 : "VT82C595/97",
0x1708 : "VIA VT1708S ",
0x1989 : "VT1708",
0x2006 : "VT6105M",
0x2012 : "1106",
0x2038 : "Unknown",
0x204 : "K8M400 chipset",
0x2204 : "???",
0x2238 : "K8T890",
0x2259 : "CN400/PM880",
0x2269 : "KT880",
0x2282 : "K8T880Pro",
0x24c5 : "8086 SoundController (ICH4-M B0 step)",
0x3009 : "SB200",
0x3038 : "VT6212L",
0x3038 : "VT8251",
0x3040 : "VT82C586A/B",
0x3041 : "82C570MV",
0x3043 : "VT86C100A",
0x3044 : "VT6307/VT6308",
0x305 : "VIA Sound VIA AC 97 in VT82C686A/B",
0x3050 : "VT82C596/596A/596",
0x3051 : "",
0x3053 : "VT6105M",
0x3057 : "VT82C686A/B",
0x3058 : "VT1709",
0x3059 : "VT 8233(AC 97 SOUND)",
0x3059 : "9739",
0x3065 : "VT6102 / VT6103",
0x3068 : "PCIVEN_1106&DEV_3068&SUBSYS_4C211543&REV_803&61A",
0x3068 : "VT82C686A/B&VT8231",
0x3068 : "VT82C686A/B&VT8231",
0x3074 : "VT8233",
0x3086 : "VT82C686",
0x3091 : "VT8633",
0x3099 : "vt8233",
0x3101 : "VT8653",
0x3102 : "VT8362",
0x3103 : "VT8615",
0x3104 : "VT6202",
0x3106 : "VT6105M/LOM",
0x3107 : "VT8233/A AC97' Enhance Audio Controller",
0x3108 : "8237",
0x3109 : "VT8233/A AC97' Enhance Audio Controller",
0x3112 : "VT8361",
0x3113 : "",
0x3116 : "VT8375",
0x3118 : "CN400",
0x3119 : "VT6120/VT6121/VT6122",
0x3122 : "3122110",
0x3123 : "VT8623",
0x3128 : "vt8753",
0x3133 : "VT3133",
0x3147 : "VT8233",
0x3148 : "VT8751",
0x3149 : "VT8237 Family/ VT6420",
0x3156 : "VT8372",
0x3157 : "VIA VT8237",
0x3158 : "",
0x3164 : "VT6410",
0x3168 : "VT8374",
0x3177 : "VT8235",
0x3178 : "",
0x3188 : "K8HTB-8237",
0x3189 : "VT8377",
0x3198 : "VEN_1106&DEV_B198&SUBSYS_00000000&REV_00",
0x3202 : "",
0x3204 : "1394 i2c",
0x3205 : "PCIVEN_1106&DEV_3108&SUBSYS_0000&REV_003&61A",
0x3208 : "PT890",
0x3209 : "",
0x3213 : "",
0x3227 : "VT8237R",
0x3230 : "K8M890CE & K8N890CE Display Driver",
0x3238 : "K8T890",
0x3249 : "VT6421",
0x3253 : "VT6655",
0x3258 : "PT880",
0x3259 : "???",
0x3269 : "KT880",
0x3282 : "K8T880Pro",
0x3288 : "040300",
0x3343 : "81CE1043",
0x3344 : "CN700",
0x3349 : "VT8251",
0x3365 : "060000A1106",
0x3371 : "P4M900",
0x3403 : "VT6315/VT6330",
0x3680 : "pciven_1106&dev_3108_&subsys_4c211543_rev_803&13",
0x401A : "VT-6325",
0x4149 : "VT6420",
0x4204 : "???",
0x4238 : "K8T890",
0x4258 : "???",
0x4259 : "???",
0x4269 : "KT880",
0x4282 : "K8T880Pro",
0x4397 : "VT1708S",
0x5000 : "3059",
0x5030 : "VT82C596",
0x5308 : "PT880 Pro / VT8237",
0x5372 : "VT8237S",
0x6100 : "VIA VT86C100A",
0x6287 : "27611",
0x7064 : "SUBSYS_10020000",
0x7204 : "K8M400",
0x7205 : "KM400",
0x7238 : "K8T890",
0x7258 : "PT880",
0x7259 : "PM800",
0x7269 : "KT880",
0x7282 : "K8T880Pro",
0x7353 : "CX700",
0x7372 : "VT8237",
0x7565 : "473040005",
0x8208 : "PT890?",
0x8231 : "VT8231",
0x8235 : "VT8754",
0x8237 : "VT8237",
0x8305 : "VT8363A/65",
0x8391 : "VT8363/71",
0x8501 : "VT8501",
0x8596 : "VT82C596",
0x8597 : "VT82C597",
0x8598 : "VT82C598",
0x8601 : "VT82C601",
0x8602 : "",
0x8605 : "VT8605",
0x8691 : "VT82C691/693A/694X",
0x8693 : "VT82C693/A",
0x8920 : "3059",
0x9238 : "K8T890",
0x9398 : "VT8601",
0x9530 : "1106",
0x9875 : "1",
0x9876 : "VT8233/A AC97' Enhance Audio Controller",
0xA208 : "PT890",
0xA238 : "K8T890",
0xb01f : "castle rock agp8x controll",
0xB091 : "VT8633",
0xB099 : "VT8366/A",
0xB101 : "VT8653",
0xB102 : "VT8362",
0xB103 : "VT8615",
0xB112 : "VT8361",
0xB113 : "",
0xB115 : "VT8363/65",
0xB116 : "VT8375",
0xB133 : "vt686b",
0xB148 : "VT8751 Apollo",
0xB156 : "VT8372",
0xB158 : "VIA Technologies Inc",
0xB168 : "VT8235",
0xB188 : "K8M800/K8N800",
0xB198 : "546546",
0xB213 : "",
0xC208 : "PT890",
0xC238 : "K8T890",
0xD208 : "PT890",
0xD213 : "",
0xD238 : "K8T890",
0xE208 : "PT890",
0xE238 : "K8T890",
0xe721 : "060000A1106",
0xe724 : "VT1705",
0xF208 : "PT890",
0xF238 : "K8T890",
},
0x1107 : { 0x8576 : "PCI Host Bridge",
},
0x1108 : { 0x0100 : "Token Ring Adapter",
0x0101 : "2-Port Token Ring Adapter",
0x0105 : "Token Ring Adapter",
0x0108 : "Token Ring Adapter",
0x0138 : "Token Ring Adapter",
0x0139 : "Token Ring Adapter",
0x013C : "Token Ring Adapter",
0x013D : "Token Ring Adapter",
},
0x1109 : { 0x1400 : "EX110TX PCI Fast Ethernet Adapter",
},
0x110A : { 0x2101 : "Multichannel Network Interface Controller for HDLC",
0x2102 : "DMA supported serial communication controller with 4 channels",
0x2104 : "PCI Interface for Telephony/Data Applications PITA-2",
0x3141 : "PROFIBUS Communication Processor CP5611 A2",
0x4033 : "EB400 ProfiNet Device-Kit",
0x4036 : "simens i/o control",
},
0x110B : { 0x0001 : "Media Processor",
0x0002 : "MPACT DVD decoder.",
0x0004 : "Integrated video card",
},
0x1112 : { 0x2200 : "FDDI adapter",
0x2300 : "Fast Ethernet adapter",
0X2340 : "4 Port 10/100 UTP Fast Ethernet Adapter",
0x2400 : "ATM adapter",
},
0x1113 : { 0x1211 : " EN5038",
0x1216 : "accton EN5251BE",
0x1217 : "Ethernet Adapter",
0x5105 : "untuk install driver",
0x9211 : "Fast Ethernet Adapter",
0x9511 : "0445tabgf16143.1",
0x9876 : "Ethernet Controller/ drivers",
},
0x1114 : { 0x0506 : "802.11b Wireless Network Adaptor",
0x3202 : "TPM - Trusted Platform Module",
},
0x1116 : { 0x0022 : "DT3001",
0x0023 : "DT3002",
0x0024 : "DT3003",
0x0025 : "DT3004",
0x0026 : "Dt3005",
0x0027 : "DT3001-PGL",
0x0028 : "DT3003-PGL",
},
0x1117 : { 0x9500 : "max-lc SVGA card",
0x9501 : "MaxPCI image processing board",
},
0x1119 : { 0x0000 : "PCI SCSI RAID Controller",
0x0001 : "PCI 1-channel SCSI RAID Controller",
0x0002 : "PCI 1-channel SCSI RAID Controller",
0x0003 : "PCI 2-channel SCSI RAID Controller",
0x0004 : "PCI 3-channel SCSI RAID Controller",
0x0005 : "PCI 5-channel SCSI RAID Controller",
0x0006 : "Wide Ultra SCSI Controller",
0x0007 : "Wide Ultra SCSI Controller",
0x0008 : "Wide Ultra SCSI Controller",
0x0009 : "Wide Ultra SCSI Controller",
0x000A : "Ultra SCSI Controller",
0x000B : "Wide SCSI Controller",
0x000C : "Wide SCSI Controller",
0x000D : "Wide SCSI Controller",
0x0100 : "2 Channel Wide Ultra SCSI",
0x0101 : "Wide Ultra SCSI HBA",
0x0102 : "Wide Ultra SCSI HBA",
0x0103 : "Wide Ultra SCSI HBA",
0x0104 : "Ultra SCSI HBA",
0x0105 : "Ultra SCSI HBA",
0x0110 : "Wide Ultra SCSI HBA",
0x0111 : "Wide Ultra SCSI HBA",
0x0112 : "Wide Ultra SCSI HBA",
0x0113 : "Wide Ultra SCSI HBA",
0x0114 : "Ultra SCSI HBA",
0x0115 : "Ultra SCSI HBA",
0x0118 : "Wide Ultra2 SCSI HBA",
0x0119 : "Wide Ultra2 SCSI HBA",
0x011A : "Wide Ultra2 SCSI HBA",
0x011B : "Wide Ultra2 SCSI HBA",
0x0120 : "",
0x0121 : "",
0x0122 : "",
0x0123 : "",
0x0124 : "",
0x0125 : "",
0x0136 : "",
0x0137 : "Disk Array Controller",
0x0138 : "",
0x0139 : "0139",
0x013A : "IBM IXA - Integrated xSeries Adapter",
0x013B : "",
0x013C : "",
0x013D : "",
0x013E : "",
0x013F : "",
0x0166 : "",
0x0167 : "",
0x0168 : "64-bit PCI Wide Untra2 SCSI HBA",
0x0169 : "64-bit PCI Wide Ultra2 SCSI HBA",
0x016A : "64-bit PCI Wide Ultra2 SCSI HBA",
0x016B : "64-bit PCI Wide Ultra2 SCSI HBA",
0x016C : "",
0x016D : "",
0x016E : "",
0x016F : "",
0x01D6 : "GDT 4513RZ",
0x01D7 : "",
0x01db : "SCSI Ultra320 1-channel",
0x01F6 : "",
0x01F7 : "BtYVKixCnmzB",
0x01FC : "cfa-4k",
0x01FD : "",
0x01FE : "",
0x01FF : "",
0x0210 : "Fibre Channel HBA",
0x0211 : "Fibre Channel HBA",
0x0260 : "64-bit PCI Fibre Channel HBA",
0x0261 : "64-bit PCI Fibre Channel HBA",
0x0300 : "",
0x6111 : "61xx raid",
},
0x111A : { 0x0000 : "",
0x0002 : "",
0x0003 : "ATM Adapter",
},
0x111C : { 0x0001 : "Powerbus Bridge",
},
0x111D : { 0x0001 : "NICStAR ATM Adapter",
0x0003 : "MICRO ABR SAR PCI ATM Controller",
0x0004 : "MICRO ABR SAR PCI ATM Controller",
0x7603 : "IDT High Definition Audio CODECj",
0x7605 : "IDT High Definition Audio CODEC",
0x7608 : "IDT High Definition Audio CODEC",
0x7616 : "SigmaTel High Definition Audio CODEC",
0x7618 : "SigmaTel High Definition Audio CODEC",
0x7621 : "IDT High Definition Codec",
0x7634 : "IDT/Sigmae HDl Audio Driver v6.10.5939.0 05/06/2008",
0x7662 : "IDT/Sigmae HDl Audio Driver v6.10.5939.0 05/06/2008",
0x7667 : "High Definition (HD) Audio Codecs",
0x7675 : "92HD73C1",
0x7680 : "SIGMATEL STAC 92XX ",
0x76A0 : "STAC 92XX C-Major HD Audio (Dell Precision M4300 and LAT D630 & D830)",
0x76B2 : "IDT Audio",
0x76D1 : "IDT High Definition Audio CODEC",
0x76D5 : "IDT 92HD87B1/3",
0x76E7 : "HDAUDIO",
0x8018 : "PCI Express Switch",
0x802d : "PCI Express Switch PES16T7",
0x806e : "PCI Express Gen2 Switch",
0x8086 : "NICStAR ATM Adapter",
0x9876 : "IDT/Sigmatel HDl Audio Driver v6.10.5939.0 05/06/2008",
},
0x111F : { 0x4A47 : "Video engine interface",
0x5243 : "Frame Capture Bus Interface",
},
0x1127 : { 0x0200 : "ATM",
0x0210 : "ATM",
0x0250 : "ATM",
0x0300 : "ATM adapter",
0x0310 : "ATM",
0x0400 : "ATM Adapter",
0x1603 : "atm",
},
0x112D : { 0x8086 : "PCI",
},
0x112E : { 0x0000 : "EIDE/hdd and IDE/cd-rom Ctrlr",
0x000B : "EIDE/hdd and IDE/cd-rom Ctrlr",
},
0x1130 : { 0xF211 : "USB Audio Sound Card",
},
0x1131 : { 0x0011 : "Ethernet Controller",
0x1001 : "BlueTooth Адаптер ISSCBTA [Tripper USB Dongle]",
0x1131 : "VerTV Hybrid Super 007 M135RA",
0x1131 : "01384E42y8",
0x1201 : "VPN IPSEC coprocessor",
0x1234 : "EHCI USB 2.0 Controller",
0x1301 : "SSL Accelerator",
0x1562 : "EHCI USB 2.0 Controller",
0x1996 : "01384E42y8",
0x2780 : "TV deflection controller",
0x3400 : "Modem",
0x3401 : "Multimedia Audio Device",
0x5400 : "Multimedia processor",
0x5400 : "Multimedia processor",
0x5402 : "Media Processor",
0x5406 : "TriMedia PNX1700",
0x7130 : "01384E42Y8",
0x7133 : "PCI audio and video broadcast decoder or only avertv dvb-t pci card",
0x7134 : "SAA7134 TV Card Philips",
0x7145 : "ddddf",
0x7146 : " 0X7146",
0x7160 : " TDA10046 and TDA8275A",
0x7162 : "idk",
0x7164 : "ASUS My Cinnema PE9400 PCI-E 1x capture card.",
0x7231 : "AVerMedia H339 Гибридный Ана",
0x9730 : "Ethernet controller",
0x9876 : "saa7146ah",
0xFFFF : "device",
},
0x1133 : { 0x7711 : "",
0x7901 : "",
0x7902 : "",
0x7911 : "",
0x7912 : "",
0x7941 : "",
0x7942 : "",
0x7943 : "EiconCard S94",
0x7944 : "EiconCard S94",
0xB921 : "",
0xB922 : "",
0xB923 : "EiconCard P92",
0xE001 : "",
0xE002 : "",
0xE003 : "",
0xE004 : "chip",
0xE005 : "Eicon ISDN card using Siemens IPAC chip",
0xE00B : "Eicon ISDN card using Infineon chip",
0xE010 : "DIVA Server BRI-2M",
0xE012 : "DIVA Server BRI-8M",
0xE013 : "DIVA Server 4BRI/PCI",
0xE014 : "DIVA Server PRI-30M",
0xE015 : "Diva Server PRI-30M PCI v.2",
0xE018 : "DIVA Server BRI-2M/-2F",
},
0x1134 : { 0x0001 : "audio driver",
0x0002 : "Dual PCI to RapidIO Bridge",
0x9876 : "audio driver",
},
0x1135 : { 0x0001 : "Printer Cntrlr",
},
0x1138 : { 0x8905 : "STD 32 Bridge",
},
0x113C : { 0x0000 : "i960 Bridge",
0x0001 : "i960 Bridge / Evaluation Platform",
0x0911 : "i960Jx I/O Controller",
0x0912 : "i960Cx I/O Controller",
0x0913 : "i960Hx I/O Controller",
0x0914 : "I/O Controller with secondary PCI bus",
},
0x113F : { 0x0808 : "Adapter",
0x1010 : "Adapter",
0x80C0 : "",
0x80C4 : "",
0x80C8 : "",
0x8888 : "",
0x9090 : "",
},
0x1141 : { 0x0001 : "EIDE/ATAPI super adapter",
},
0x1142 : { 0x3210 : "VGA/AVI Playback Accelerator",
0x6410 : "GUI Accelerator",
0x6412 : "GUI Accelerator",
0x6420 : "GUI Accelerator",
0x6422 : "ProMotion-6422",
0x6424 : "ProMotion AT24 GUI Accelerator",
0x6425 : "0752 20005",
0x6426 : "GUI Accelerator",
0x643D : "ProMotion-AT3D",
0x9876 : "139K76B 9808",
3210 : "139K76B",
},
0x1144 : { 0x0001 : "Noservo Cntrlr",
},
0x1145 : { 0xF21 : "HDCClassName=",
0xF020 : "CardBus ATAPI Host Adapter",
0xF021 : "CardBus CompactFlash Adapter",
0xf024 : "CardBus CompactFlash Adapter",
},
0x1147 : { 0x1123 : "131dq",
},
0x1148 : { 0x4000 : "FDDI adapter",
0x4200 : "Token Ring Adapter",
0x4300 : "SK-NET Gigabit Ethernet Adapter",
0x4320 : "SysKonnect Marvel RDK 8001",
0x4362 : "Marvell Yukon 88E8053 based Ethernet Controller",
0x9000 : "PCI-X 10/100/1000Base-T Server",
0x9E00 : "PCI Express 10/100/1000Base-T Desktop",
},
0x114A : { 0x5565 : "Ultrahigh-Speed Fiber-Optics Reflective Memory w/ Interrupts",
0x5579 : "Reflective Memory Card",
0x5588 : "VMICPCI5588 Reflective Memory Card",
0x6504 : "Timer/SRAM FPGA",
0x7587 : "",
},
0x114D : { 0x2189 : "PCTel HSP56 PCI Modem",
},
0x114F : { 0x0002 : "ACPINSC6001",
0x0003 : "",
0x0004 : "driver",
0x0005 : "",
0x0006 : "",
0x0007 : "Digi Data Fire PCI 1 S/T",
0x0009 : "",
0x000A : "",
0x000C : "",
0x000D : "X.25/FR 2-port",
0x0011 : "",
0x0012 : "",
0x0013 : "",
0x0014 : "",
0x0015 : "",
0x0016 : "",
0x0017 : "",
0x0019 : "",
0x001A : "",
0x001B : "",
0x001D : "T1/E1/PRI",
0x001F : "ClydeNonCsu6034",
0x0020 : "ClydeNonCsu6032",
0x0021 : "ClydeNonCsu4",
0x0022 : "ClydeNonCsu2",
0x0023 : "",
0x0024 : "",
0x0026 : "",
0x0027 : "",
0x0029 : "",
0x0034 : "",
0x0035 : "T1/E1/PRI",
0x0040 : "",
0x0042 : "",
0x0070 : "",
0x0071 : "Descargar",
0x0072 : "",
0x0073 : "",
0x00c8 : "Digi Neo 2",
0x6001 : "ACPIVEN_HPQ&DEV_6001",
},
0x1155 : { 0x0810 : "486 CPU/PCI Bridge",
0x0922 : "Pentium CPU/PCI Bridge",
0x0926 : "PCI/ISA Bridge",
},
0x1158 : { 0x3011 : "Tokenet/vg 1001/10m anylan",
0x9050 : "Lanfleet/Truevalue",
0x9051 : "Lanfleet/Truevalue",
},
0x1159 : { 0x0001 : "",
0x0002 : "Frame Grabber",
},
0x115D : { 0x0003 : "Cardbus Ethernet 10/100+Modem 56",
0x0005 : "CardBus Ethernet 10/100",
0x0007 : "CardBus Ethernet 10/100",
0x000B : "CardBus Ethernet 10/100",
0x000C : "Mini-PCI V.90 56k Modem",
0x000F : "CardBus Ethernet 10/100",
0x002b : "Winmodem built into NEC Versa VXi",
0x0076 : "Xircom MPCI3B-56G (Lucent SCORPIO) Soft",
0x00d3 : "Xircom MPCI Modem 56",
0x00D4 : "Modem 56k",
0x0101 : "CardBus 56k Modem",
0x0103 : "CardBus Ehternet + 56k Modem",
},
0x1161 : { 0x0001 : "Host Bridge",
},
0x1163 : { 0x0001 : "3D Blaster",
0x2000 : "Rendition V2200 (BLITZ 2200 AGP)",
},
0x1165 : { 0x0001 : "Motion JPEG rec/play w/audio",
0x0060 : "Foresight Imaging I-Color",
},
0x1166 : { 0x0005 : "PCI to PCI Bridge",
0x0006 : "Host Bridge",
0x0007 : "CPU to PCI Bridge",
0x0008 : "Hostbridge & MCH",
0x0009 : "AGP interface",
0x0010 : "",
0x0011 : "",
0x0012 : "",
0x0013 : "Hostbridge and MCH",
0x0014 : "Host Bridge",
0x0015 : "Hostbridge and MCH",
0x0016 : "Host Bridge",
0x0017 : "",
0x0101 : "",
0x0103 : " ",
0x0110 : "I/O Bridge with Gigabit Ethernet ServerWorks Grand Champion",
0x0200 : "PCI to ISA Bridge",
0x0201 : "ISA bridge",
0x0203 : "PCI to ISA Bridge",
0x0211 : "PATA33 Controller",
0x0212 : "PATA66",
0x0213 : "PATA100 RAID Controller",
0x0217 : "PATA100 IDE Controller",
0x0220 : "OpenHCI Compliant USB Controller",
0x0221 : "OHCI Compliant USB Controller",
0x0223 : "USB controller",
0x0225 : "PCI Bridge",
0x0227 : "PCI Bridge",
0x0230 : "PCI to ISA bridge",
0x0240 : "Apple K2 SATA AHCI&RAID Controller",
0x0241 : "ServerWorks Frodo4 SATA RAID Controller",
0x0242 : "ServerWorks Frodo8 8xSATA RAID",
0x024A : "Broadcom5785/Serverworks HT1000 AHCI Controller",
0x024B : "BC5785/ServerWorks HT1000 SATA(IDE MODE)",
0x0252 : "ServerWorks Elrond 8xSAS/SATAII",
},
0x1168 : { 0x7145 : "ATI Mobility Radeon X 1400",
},
0x1169 : { 0x0102 : "32 Channel Digital Input Card Interface",
0x0202 : "16 Channel Digital Output",
0x0302 : "32 Channel Analog Input Interface",
0x0402 : "16 Channel Analog Output / Analog Input Interface",
0x0502 : "8 Channel Timer Counter Interface",
0x0902 : "PCI to TigerSHARC FPGA Interface",
0x2001 : "PCI to C-DAC RTU bus interface FPGA",
},
0x116A : { 0x6100 : "",
0x6800 : "",
0x7100 : "",
0x7800 : "nvidia harmony",
},
0x116E : { 0x0015 : "Fiery EX2000D RIP Card Melbourne VX120",
0x0500 : "Printer ASIC",
},
0x1172 : { 0x0001 : "S CCA5000243A",
0x0004 : "Multi-serial card",
0x0007 : "Altera FPGA board",
0x1234 : "Stratix V FPGA",
0xD4AA : "Arria GX",
},
0x1176 : { 0x8474 : "Conexant Multichannel Synchronous Communications Controller (MUSYCC)",
},
0x1178 : { 0xAFA1 : "Fast Ethernet",
},
0x1179 : { 0x8136 : "Realtek 10/100/1000 PCI-E NIC Family",
0x0102 : "Trusted Platform Module",
0x0103 : "Extended PCI IDE Controller Type-B",
0x0117 : "PCIVEN_10EC&DEV_8136&SUBSYS_184103C&REV_054&87C21B2&0&00E3",
0x0404 : "",
0x0406 : "Video Capture device",
0x0407 : "",
0x0601 : "Toshiba CPU to PCI bridge",
0x0602 : "PCI to ISA Bridge for Notebooks",
0x0603 : "PCI to CardBus Bridge for Notebooks",
0x0604 : "PCI to PCI Bridge for Notebooks",
0x0605 : "PCI to ISA Bridge for Notebooks",
0x0606 : "PCI to ISA Bridge for Notebooks",
0x0609 : "PCI to PCI Bridge for Notebooks",
0x060A : "Toshiba ToPIC95 CardBus Controller",
0x060F : "CardBus Controller",
0x0611 : "PCI-ISA Bridge",
0x0617 : "PCI to CardBus Bridge with ZV support",
0x0618 : "CPU to PCI and PCI to ISA Bridge",
0x0701 : "PCI Communication Device",
0x0804 : "Toshiba Smart Media Host Controller",
0x0805 : "ACPITOS62052&DABA3FF&1",
0x0D01 : "FIR Port Type-O",
0x1179 : "Dispositivo de comunicaciones pci",
0x13A8 : "Multi-channel PCI UART",
0x3b64 : "Management Engine Driver",
0x8136 : "pciven_10 EC & DEV_8136 & SUBSYS_FF IE 1179 & REV_05",
0x9876 : "SD Card Controller",
},
0x117B : { 0x8320 : "VGA",
},
0x117C : { 0x0030 : "Dual-Channel Low-Profile Ultra320 SCSI PCIe Host Bus Adapter",
0x0042 : "Low-Profile 16-Internal Port 6Gb/s SAS/SATA PCIe 2.0 Host Bus Adapter",
},
0x117E : { 0x0001 : "Printer Host",
},
0x1180 : { 0x0475 : "Cardbus Controller",
0x0476 : "RICOH SmartCard Reader",
0x0478 : "Cardbus Controller",
0x0552 : "FireWire (IEEE 1394) Controller",
0x0575 : "I11fXI <a href=",
0x059 : "1",
0x0592 : "Ricoh R5C833 R5C8xx Memory Stick Controller",
0x05 : "Ricoh R5U8xx Card Reader Driver - Win xp",
0x0822 : "SDA Standard Compliant SD Host Controller",
0x0832 : "ACPIENE01004&15458EF3&0",
0x0843 : "Ricoh SD Host Controller",
0x0847 : "delete",
0x0852 : "Ricoh xD-Picture Card Controller",
0x1108 : "Ricoh Memory Stick Host Controlle",
0x2792 : "PCIVEN_8086&DEV_0083&SUBSYS_13058086&REV_00",
0x5551 : "IEEE 1394 Controller",
0x852 : "Ricoh xD-Picture Card Host Controller;0852h xd picture card controller",
0x9876 : "Ricoh Memory Stick Host Controlle",
0x9876 : "Ricoh SD/Host Controller",
0xE203 : "Ricoh PCIe Memory Stick Host Controller",
0xE230 : "Ricoh PCIe Memory Stick Host Controller",
0xe476 : "Multipurpose chip",
0xe822 : "Ricoh PCIe SD/MMC Host Controller",
0xe823 : "Ricoh PCIe SDXC/MMC Host Controller",
0xe832 : "Ricoh PCIe IEEE1394 Fireware Host Controller",
0xE852 : "Ricoh PCIe xD-Picture Card Controller",
},
0x1185 : { 0x8929 : "EIDE Controller",
},
0x1186 : { 0x0100 : "Ethernet Adapter",
0x1002 : "Fast Ethernet Adapter",
0x1100 : "Fast Ethernet Adapter",
0x1300 : "Realtek RTL8139 Family PCI Fast Ethernet Adapter",
0x1301 : "Fast Ethernet Adapter",
0x1340 : "Fast Ethernet CardBus PC Card",
0x1561 : "CardBus PC Card",
0x3065 : "D-Link DFE-500Tx PCI fast Ethernet adapter Re v.A",
0x3106 : "Fast Ethernet Adapter",
0x3300 : "IEEE 802.11g PCI card",
0x3b00 : "D-LINK DWL-650+",
0x3c09 : "Ralink RT61",
0x4000 : "Gigabit Ethernet Adapter",
0x4001 : "D Link Fast Ethernet PCMCIA Card",
0x4200 : "-",
0x4300 : "Used on DGE-528T Gigabit adaptor",
0x4302 : "DGE-530T",
0x4b00 : "D-Link System Inc DGE-560T PCI Express Gigabit Ethernet Adapter (rev 13)",
0x4B01 : "Gigabit Ethernet Adapter",
0x4C00 : "Gigabit Ethernet Adapter",
0x9876 : "d",
},
0x1189 : { 0x1592 : "VL/PCI Bridge",
},
0x118C : { 0x0014 : "C-bus II to PCI bus host bridge chip",
0x1117 : "Corollary/Intel Memory Controller Chip",
},
0x118D : { 0x0001 : "Raptor-PCI framegrabber",
0x0012 : "Road Runner Frame Grabber",
0x0014 : "Road Runner Frame Grabber",
0x0024 : "Road Runner Frame Grabber",
0x0044 : "Road Runner Frame Grabber",
0x0112 : "Road Runner Frame Grabber",
0x0114 : "Road Runner Frame Grabber",
0x0124 : "Road Runner Frame Grabber",
0x0144 : "Road Runner Frame Grabber",
0x0212 : "Road Runner Frame Grabber",
0x0214 : "Road Runner Frame Grabber",
0x0224 : "Road Runner Frame Grabber",
0x0244 : "Road Runner Frame Grabber",
0x0312 : "Road Runner Frame Grabber",
0x0314 : "Road Runner Frame Grabber",
0x0324 : "Road Runner Frame Grabber",
0x0344 : "Road Runner Frame Grabber",
},
0x118E : { 0x0042 : "",
0x0142 : "",
0x0242 : "",
0x0342 : "",
0x0440 : "",
0x0442 : "",
0x0842 : "red",
},
0x1190 : { 0x2550 : "Single Chip Ultra (Wide) SCSI Processor",
0xC721 : "EIDE",
0xC731 : "PCI Ultra (Wide) SCSI Adapter",
},
0x1191 : { 0x0001 : "IDE Ctrlr",
0x0002 : "UltraDMA33 EIDE Controller (AEC6210UF)",
0x0003 : "SCSI-2 cache Cntrlr",
0x0004 : "UltraDMA33 EIDE Controller",
0x0005 : "UltraDMA33 EIDE Controller (AEC6210UF)",
0x0006 : "UltraDMA66 EDIE Controller (AEC6260)",
0x0007 : "UltraDMA66 EIDE Controller (AEC6260)",
0x0008 : "2CH PCI UltraDMA133 IDE Controller",
0x0009 : "AEC6280PATA133|AEC6880 PATA RAID|AEC6290 SATA|AEC6890 SATA RAID|AEC6891 SATA RAID",
0x000a : "ACARD AEC-6885/6895/6896 RAID Controller",
0x000B : "ACARD AEC-6897/6898 RAID Controller",
0x000D : "2S1P PCI-X SATA(3G)/UDMA Combo Controller",
0x8001 : "SCSI-2 RAID (cache?) Adapter (AEC6820U)",
0x8002 : "AEC6710S/U/UW SCSI-2 Host Adapter ",
0x8010 : "Ultra Wide SCSI Controller",
0x8020 : "AEC6712U/TU Ultra SCSI Controller",
0x8030 : "AEC 6712S/TS Ultra SCSI Controller",
0x8040 : "SCSI Controller",
0x8050 : "AEC6715UW Ultra Wide SCSI Controller",
0x8060 : "SCSI Host Adapter/PAYPAL.COM/X.COM",
0x8081 : "PCI Ultra160 LVD/SE SCSI Adapter",
0x808A : "AEC6710S/U/UW SCSI-2 Host Adapter",
},
0x1197 : { 0x010C : "8-bit 2GS/s Analog Input Card",
},
0x1199 : { 0x0001 : "IRMA 3270 PCI Adapter",
0x0002 : "Advanced ISCA PCI Adapter",
0x0201 : "SDLC PCI Adapter",
},
0x119B : { 0x1221 : "PCI PCMCIA bridge",
},
0x119E : { 0x0001 : "FireStream 155 ATM adapter",
0x0003 : "FireStream 50 ATM adapter",
},
0x11A8 : { 0x7302 : "NTX-8023-PCI 2MB Long Card",
0x7308 : "NTX-8023-PCI 8MB Long Card",
0x7402 : "NTX-8023-PCI 2MB Short Card",
0x7408 : "NTX-8023-PCI 8MB Short Card",
},
0x11A9 : { 0x4240 : "pci matchmaker 9622qac",
},
0x11AB : { 0x0028 : "MCP67 High Definition Audio",
0x0146 : "System Ctrlr for R4xxx/5000 Family CPUs",
0x11AB : "Gigabit Ethernet Controller",
0x11AB : "Marvell Yukon 88E8055 PCI-E Gigabit Ethernet Controller",
0x11AB : "Gigabit Ethernet Controller",
0x13F8 : "802.11 Adapter",
0x1fa6 : "The Libertas WLAN 802.11b/g",
0x1FA7 : "Libertas WLAN 802.11b/g",
0x1fa8 : "54M Wireless 802.11b PCI wifi Adapter Card",
0x1FAA : "Nexxt Solution Wireless 11/54mbps NW122NXT12",
0x2A30 : "PCI-Express 802.11bg Wireless",
0x4320 : "Marvell Yukon PCI E Gigabit drivers for d",
0x4350 : "Yukon PCI-E Fast Ethernet Controller",
0x4351 : "Yukon PCI-E Fast Ethernet Controller",
0x4352 : "Marvell Yukon 88E8038 PCI-E Fast Ethernet Controller",
0x4353 : "Gigabit",
0x4354 : "Marvell Yukon 88E8040 PCI-E Fast Ethernet Controller",
0x4355 : "Marvell Yukon 88E8040T PCI-E Fast Ethernet Controller",
0x4357 : "marvell ethernet lan No painel ",
0x4360 : "Yukon PCI-E ASF Gigabit Ethernet Controller",
0x4361 : "Marvell Yukon 88E8036 Network Card",
0x4362 : "Marvell Yukon 88E8053 PCI-E Gigabit Ethernet Controller",
0x4363 : "Yukon PCI-E Gigabit Ethernet Controller",
0x4364 : "Yukon PCI-E Gigabit Ethernet Controller",
0x4365 : "Yukon Gigabit Controller DRIVER",
0x436A : "Marvell Yukon 88E8058",
0x436b : "Marvell Yukon 8072",
0x436b : "Marvell Yukon PCI-E Gigabit Ethernet Controller",
0x436C : "Marvell 8072 Ethernet Nic",
0x4380 : "Marvell Yukon 88E8057 PCI-E Gigabit Ethernet Controller",
0x4381 : "Marvell Yukon 88E8059 PCI-E Gigabit Ethernet Controller",
0x4611 : "System Controller",
0x4620 : "System Controller for R5000 & R7000 (64-bit PCI)",
0x4801 : "8 port switched ethernet ctrlr",
0x4809 : "Evaluation board for the GT-48300",
0x5005 : "Belkin Desktop Gigabit PCI card",
0x5040 : "4-port SATA I PCI-X Controller",
0x5041 : "4-port SATA I PCI-X Controller",
0x5080 : "SATA Controller",
0x5081 : "SATA Controller",
0x6041 : "Marvell Technology Group Ltd. MV88SX6041 4-port SATA II PCI-X Controller (rev 03)",
0x6081 : "PCI-X RocketRAID 222x SATA Controller",
0x6101 : "PATA 133 One Channel",
0x6111 : "61xx RAID",
0x6120 : "61xx RAID",
0x6121 : "61xx AHCI",
0x6122 : "61xx RAID",
0x6140 : "61xx RAID",
0x6145 : "Add-on IC to provide 4x SATA Ports",
0x6320 : "System Controller for PowerPC Processors",
0x6440 : "64xx/63xx SAS",
0x6480 : "PowerPC System Controller",
0x6485 : "Marvel 88SE6480 is the chip on the mainboard",
0x9128 : "SATA3 6 GB/s SATA3/Raid Controller",
0x91A2 : "Sata 6G RAID Controller",
0x9653 : "Advanced Communication Controller",
0x9876 : "marvell yukon 88E8038 pci-e fast ethernet controller",
0xF003 : "Primary Image Piranha Image Generator",
0xF004 : "Primary Image Barracuda Image Generator",
0xF006 : "Primary Image Cruncher Geometry Accelerator",
0xFFFF : "PATA2SATA/SATA2PATA Bridge",
},
0x11AD : { 0x0001 : "Fast Ethernet Adapter",
0x0002 : "NETGEAR FA310TX Fast Ethernet PCI Adapter",
0xC115 : "PNIC II PCI MAC/PHY",
},
0x11AE : { 0x4153 : "Bridge Controller",
0x5842 : "Bridge Controller",
},
0x11AF : { 0x0001 : "9704",
0x000A : " ",
0x000B : " ",
},
0x11B0 : { 0x0001 : "i960 Local Bus to PCI Bridge",
0x0002 : "i960Jx Local Bus to PCI Bridge",
0x0004 : "i960Cx/Hx Local Bus to PCI Bridge",
0x0010 : "Am29K Local Bus to PCI Bridge",
0x0021 : "i960Sx Local Bus to PCI Bridge",
0x0022 : "i960Jx Local Bus to PCI Bridge",
0x0024 : "i960Cx/Hx Local Bus to PCI Bridge",
0x0030 : "Am29K Local Bus to PCI Bridge",
0x0100 : "PCI System Ctrlr for 32-bit MIPS CPU",
0x0101 : "PCI System Ctrlr for 32-bit MIPS CPU",
0x0102 : "PCI System Ctrlr for Super-H SH3 CPU",
0x0103 : "PCI System Ctrlr for Super-H SH4 CPU",
0x0200 : "High Performance PCI SDRAM Controller",
0x0292 : "Am29030/40 Bridge",
0x0500 : "PCI System Ctrlr for 64-bit MIPS CPU",
0x0960 : "i960 Bridges for i960 Processors",
0x4750 : "SCRAMNet",
0xC960 : "i960 Dual PCI Bridge",
},
0x11B5 : { 0x0001 : "1553 Bus Interface Card",
0x0002 : "FLASH memory Card",
0x0003 : "Multi Media Adapter",
0x0004 : "Video Graphics Overlay",
0x0005 : "PPzero Slave Interface Card",
0x0006 : "PPzero Master Interface Card",
0x0007 : "Serial/1553 Interface Card",
0x0008 : "Intelligent Serial/Ethernet Card",
0x0009 : "Parallel I/O Module",
0x000a : "Fibre Channel Adapter",
0x000b : "High Speed DSP Gateway Module",
0x000c : "Memory Adaptor Module",
0x0012 : "FLASH memory Card (V2)",
0x0013 : "1553 Bus Interface Card",
0x0014 : "1553 Bus Interface Card",
0x2200 : "Dual Fibre Channel Adapter",
},
0x11B8 : { 0x0001 : "",
},
0x11B9 : { 0xC0ED : "",
},
0x11BC : { 0x0001 : "PCI FDDI",
},
0x11BD : { 0x0015 : "rob2d",
0x1111 : "www.unibobodioulasso.0fees.net",
0x1158 : "Tunner Royal TS 1",
0x11BD : "maintenance informatique",
0x11 : "Tunner Royal TS 2",
0x2020 : "70009823/76199706",
0xBEBE : "MAINTENANCE INFORMATIQUE VENTE DE CONSOMABLE",
0xBEDE : "Pinnacle Studio 700 PCI",
},
0x11C1 : { 0x0440 : "Data+Fax+Voice+DSVD",
0x0441 : "modem driver",
0x0442 : "LT WinModem 56K Data+Fax",
0x0443 : "1646T00",
0x0444 : "845G",
0x0445 : "",
0x0446 : "PCIVEN_10DE&DEV_03d1&subsys_26011019&rev_a23&2411e6fe&0&68",
0x0447 : "windowsme",
0x0448 : "SV2P2",
0x0449 : "0449144F",
0x044A : "pci ven_1904",
0x044B : "USBVID_13FD&PID_1650&REV_0446",
0x044C : "SV95PL-TOO",
0x044D : "",
0x044E : "LT WinModem 56k Data+Fax or Agere F-1156IV/A3",
0x044F : "LT V.90+DSL WildFire Modem",
0x0450 : "LT Winmodem 56K",
0x0451 : "LT WinModem 56k Data+Fax+Voice+DSVD",
0x0452 : "1513144",
0x0453 : "",
0x0454 : "",
0x0455 : "",
0x0456 : "",
0x0457 : "",
0x0458 : "Mars 3 Mercury v.92 v.44",
0x0459 : "",
0x045A : "",
0x045D : "mars2",
0x0461 : "V90 Wildfire Modem",
0x0462 : "56K.V90/ADSL Wildwire Modem",
0x0464 : "Lucent Wildwire v.90 + DSL modem",
0x0480 : "56k.V90/ADSL Wildfire Modem",
0x048b : "creative modem blaster di5733-1",
0x048C : "net-comm modem",
0x048d : "9m56pml-g",
0x048E : "56k V.92modem",
0x048F : "Agere PCI Soft Modem. SV92PL",
0x0540 : "",
0x0600 : "SV92P-T00 Agere PCI Soft Modem. SV92PL",
0x0620 : "Agere PCI Soft Modem ",
0x0630 : "#1: 32 pins",
0x1040 : "Agere Systems HDA Modem",
0x11c1 : "Agere Systems HDA",
0x3026 : "Agere Modem",
0x3055 : "Agere Systems HDA Modem v6081",
0x4758 : "Mach64 GX",
0x5400 : "FPSC FPGA with 32/64bit",
0x5801 : "USB Open Host Controller",
0x5802 : "2-port PCI-to-USB OpenHCI Host Ctrlr",
0x5803 : "QuadraBus 4-port USB OpenHCI Host Ctrlr",
0x5805 : "USB Advanced Host Controller",
0x5811 : "1394A PCI PHY/Link Open Host Ctrlr I/F",
0x5901 : "firewire chip for macbook pro",
0x9876 : "LT WinModem 56K Data+Fax",
0xAB20 : "PCI Wireless LAN Adapter",
0xAB30 : "Mini-PCI WaveLAN a/b/g",
0xED00 : "PCI-E Ethernet Controller",
7121 : "",
00 : "",
},
0x11C6 : { 0x3001 : "VM-1200 Opto Unit Controller",
},
0x11C8 : { 0x0658 : "32 bit ",
0xD665 : "64 bit ",
0xD667 : "64 bit ",
},
0x11C9 : { 0x0010 : "16-line serial port w/DMA",
0x0011 : "4-line serial port w/DMA",
},
0x11CB : { 0x2000 : "port small IC",
0x4000 : "XIO/SIO Host",
0x8000 : "Bridge RIO Host",
},
0x11CE : { 0x102B : "FF00102B",
},
0x11D1 : { 0x01F7 : "PCI Video Processor",
0x01F8 : "PCI Video Processor",
0x01f9 : "tuner card",
0x520 : "Video card",
},
0x11D4 : { 0x11D4 : "AD1988B",
0x11d4 : "266e&subsys",
0x1535 : "ADSP-21535",
0x1805 : "62412-51",
0x1884 : "AD1884HD",
0x1889 : "AD1980",
0x194A : "AD1984A",
0x1981 : "7037",
0x1983 : "AD1983HD",
0x1984 : "Analog Devices ADI 1984",
0x1986 : "ADI1986A",
0x1988 : "AD1981",
0x198B : "AD1988B",
0x2192 : "ADSP-2192",
0x219A : "ADSP-2192",
0x219E : "ADSP-2192",
0x2F44 : "ADSP-1882",
0x989B : "AD1989B",
},
0x11D5 : { 0x0115 : "Versatec Parallel Interface (VPI) + Centronics",
0x0116 : "DR11-W emulator",
0x0117 : "Versatec Parallel Interface (VPI) + Centronics",
0x0118 : "DR11-W emulator",
},
0x11DA : { 0x2000 : "Virtual-Bus / AlacrityVM bridge",
},
0x11DB : { 0x1234 : "Dreamcast Broadband Adapter",
},
0x11DE : { 0x6057 : "AV PCI Controller - Pinnacle DC10plus",
0x6067 : "zoran",
0x6120 : "MPEG VideoBVPSXI Capture Card",
0x6057 : "ZORAN PCI Bridge (interface for transferring video across the PCI bus)",
0x9876 : "",
},
0x11EC : { 0x0028 : "MCP67 High Definition Audio",
0x2064 : "",
},
0x11F0 : { 0x4 : "PCIVEN_8086&DEV_2772&SUBSYS_0CCB105B&REV_023&2411E6FE&0&10",
0x4231 : "2",
0x4232 : "PCIVEN_8086&DEV_2772&SUBSYS_0CCB105B&REV_023&2411E6FE&0&10",
0x4233 : "",
0x4234 : "",
0x4235 : "",
0x4236 : "",
0x4731 : "Gigabit Ethernet Adapter",
0x9876 : "2",
},
0x11F4 : { 0x2915 : "",
},
0x11F6 : { 0x0112 : "ReadyLink ENET100-VG4",
0x0113 : "FreedomLine 100",
0x1401 : "ReadyLink RL2000",
0x2011 : "ReadyLink RL100ATX/PCI Fast Ethernet Adapter",
0x2201 : "ReadyLink 100TX (Winbond W89C840)",
0x9881 : "ReadyLink RL100TX Fast Ethernet Adapter",
},
0x11F8 : { 0x7364 : "FREEDM-32 Frame Engine & Datalink Mgr",
0x7366 : "FREEDM-8 Frame Engine & Datalink Manager",
0x7367 : "FREEDM-32P32 Frame Engine & Datalink Mgr",
0x7375 : "LASAR-155 ATM SAR",
0x7380 : "FREEDM-32P672 Frm Engine & Datalink Mgr",
0x7382 : "FREEDM-32P256 Frm Engine & Datalink Mgr",
0x7384 : "FREEDM-84P672 Frm Engine & Datalink Mgr",
0x8000 : "6G SAS/SATA Controller",
0x8010 : "6G SAS/SATA RAID Controller",
},
0x11FB : { 0x0417 : "PCI-417 High Speed A/D Board",
},
0x11FE : { 0x0001 : "",
0x0002 : "",
0x0003 : "",
0x0004 : "",
0x0005 : "",
0x0006 : "",
0x0007 : "",
0x0008 : "",
0x0009 : "",
0x000A : "",
0x000B : "",
0x000C : "",
0x000D : "",
0x8015 : "4-port UART 16954",
},
0x1202 : { 0x0001 : "PCI ATM Adapter",
},
0x1203 : { 0x0001 : "Unknown",
},
0x1204 : { 0x9876 : "wwDW",
},
0x1208 : { 0x4853 : "HS-Link Device",
},
0x1209 : { 0x0100 : "PLX PCI BRIDGE",
},
0x120E : { 0x0100 : "Multiport Serial Card",
0x0101 : "Multiport Serial Card",
0x0102 : "Multiport Serial Card",
0x0103 : "Multiport Serial Card",
0x0104 : "Multiport Serial Card",
0x0105 : "Multiport Serial Card",
0x0200 : "Intelligent Multiport Serial",
0x0201 : "Intelligent Serial Card",
0x0300 : "1105",
0x0301 : "",
0x0302 : "",
0x0303 : "teclado",
},
0x120F : { 0x0001 : "",
},
0x1210 : { 0x25f4 : "No data",
},
0x1216 : { 0x0003 : "PTM400 PCI Taxi Module",
},
0x1217 : { 0x00f7 : "1394 Open Host Controller Interface",
0x1217 : "111111111",
0x6729 : "PCI to PCMCIA Bridge",
0x673A : "PCI to PCMCIA Bridge",
0x6832 : "CardBus Controller",
0x6836 : "CardBus Controller",
0x6872 : "CardBus Controller",
0x6925 : "CardBus Controller",
0x6933 : "CardBus Controller",
0x6972 : "CardBus Controller",
0x7110 : "MemoryCardBus Accelerator",
0x7112 : "",
0x7113 : "PCMCIA/SmartCardBus Contoller",
0x7114 : "CardBus Controller",
0x7120 : "O2Micro Integrated MMC/SD controller",
0x7130 : "O2Micro Integrated MMC/SD/MS/xD/SM Controller",
0x7134 : "MemoryCardBus Controller 6-in-1",
0x7135 : "MemoryCardBus Contoller",
0x7136 : "O2Micro CardBus Controller",
0x71E2 : "",
0x7212 : "",
0x7213 : "",
0x7222 : "pci to pcmcia bridge",
0x7223 : "MemoryCardBus Controller",
0x8130 : "o2 sd card reader",
0x8231 : "O2Micro OZ600XXX Memory Card ",
0x8330 : "Mass storage controller [0180]",
0x8331 : "O2Micro Integrated MS/PRO controller",
},
0x121A : { 0003 : "",
003 : "",
0x0001 : "Voodoo 3D Acceleration Chip",
0x0002 : "Voodoo 2 3D Accelerator",
0x0003 : "Voodoo Banshee",
0x0005 : "All Voodoo3 chips",
0x0007 : "",
0x0009 : "AGP X2",
0x0010 : "Rev.A AGPx4",
0x0057 : "Avenger",
},
0x1220 : { 0x1220 : "AMCC 5933 TMS320C80 DSP/Imaging Board",
0x4242 : "controller audio multimediale",
},
0x1223 : { 0x0001 : "KatanaQp",
0x0002 : "KosaiPM",
0x0016 : "PCIe-8120",
0x003 : "Katana3752",
0x004 : "Katana3750",
0x0044 : "Memory controller",
0x005 : "Katana752i",
0x006 : "Katana750i",
0x007 : "CC1000dm",
0x008 : "Pm3Gv",
0x009 : "Pm3GE1T1",
0x010 : "SpiderwareSG",
0x011 : "SpiderwareSS7",
0x012 : "SpiderSS7",
0x013 : "Spider FRAME RELAY",
0x014 : "Spider STREAMS",
0x015 : "Spider DSF",
},
0x1224 : { 0x1000 : "Plum Audio",
},
0x122D : { 0x1206 : "Asus",
0x4201 : "AMR 56K modem",
0x50DC : "Audio",
0x80DA : "Audio",
},
0x122F : { 0x37AF : "Reflectometer using PLX 9030",
},
0x1236 : { 0x0000 : "RealMagic64/GX",
0x0531 : "MX98715/25",
0x3d01 : "000",
0x6401 : "REALmagic64/GX",
0x9708 : "realmagic64/gx",
},
0x123D : { 0x0010 : "PCI-DV Digital Video Interface",
},
0x123F : { 0x00E4 : "MPEG",
0x6120 : "DVD device",
0x8120 : "i440B",
0x8888 : "cPEG C 3.0 DVD/MPEG2 Decoder",
},
0x1241 : { 0x1603 : "keyboard",
},
0x1242 : { 0x1460 : "2-Gb/s Fibre Channel-PCI 64-bit 66 MHz",
0x1560 : "Dual Channel 2 Gb/s Fibre Channel-PCI-X",
0x4643 : "JNI PCI 64-bit Fibrechannel (needs clone)",
},
0x1244 : { 0x0700 : "ISDN controller",
0x0800 : "ISDN Controller",
0x0A00 : "ISDN Controller",
0x0E00 : "Fritz!PCI 2.0 ISDN Controller",
0x1100 : "ISDN Controller",
0x1200 : "ISDN Controller",
0x2700 : "DSP TNETD5100GHK / TNETD5015",
0x2900 : "AVM Fritz!Card DSL v2.0 PCI",
},
0x124A : { 0x10BD : "Intel Gigabit network connection",
0x4023 : "Blitzz Wireless G",
},
0x124C : { 0x0220 : ".",
},
0x124D : { 0x0000 : "",
0x0002 : "",
0x0003 : "",
},
0x124F : { 0x0041 : "PCI RAID Controller",
},
0x1250 : { 0x1978 : "",
0x2898 : "",
},
0x1255 : { 0x1110 : "",
0x1210 : "",
0x2110 : "VideoPlex pci bpc1825 rev a",
0x2120 : "VideoPlex BPC 1851 A",
0x2130 : "",
},
0x1256 : { 0x4201 : "EIDE Adapter",
0x4401 : "Dale EIDE Adapter",
0x5201 : "IntelliCache SCSI Adapter",
},
0x1258 : { 0x1988 : "",
},
0x1259 : { 0x2503 : "",
0x2560 : "AT-2560 Fast Ethernet Adapter (i82557B)",
0xc107 : "",
},
0x125B : { 0x0B95 : "USB2.0 to 10/100M Fast Ethernet Controller",
0x1400 : "ASIX AX88140 Based PCI Fast Ethernet Adapter",
0x1720 : "USB2 to Fast Ethernet Adapter",
},
0x125D : { 0x0000 : "PCI Fax Modem (early model)",
0x1961 : "ESS Solo-1 Soundcard",
0x1968 : "Maestro-2 PCI audio accelerator",
0x1969 : "Solo-1 PCI AudioDrive family",
0x1978 : "ESS Maestro-2E PCI Audiodrive",
0x1980 : "subsys_0012103c_rev_12",
0x1988 : "ESS Allegro PCI Audio (WDM)",
0x1989 : "ESS Maestro 3 PCI Audio Accelerator",
0x1990 : "",
0x1992 : "",
0x1998 : "Maestro 3i",
0x1999 : "TAWE0548S",
0x199B : "Maestro-3.COMM PCI Voice+audio",
0x2808 : "PCI Fax Modem (later model)",
0x2828 : "TeleDrive",
0x2838 : "PCI Data Fax Modem",
0x2839 : "Superlink Modem/V.92 chipset 56K",
0x2898 : "TelDrive ES56T-PI family V.90 PCI modem",
},
0x125F : { 0x2084 : "AMCC Bridge + 2 x Super I/O (National PC97338)",
},
0x1260 : { 0x3860 : "PRISM 2.5 802.11b 11Mbps Wireless Controller",
0x3872 : "LAN-Express IEEE 802.11b PCI Adapter",
0x3873 : "PRISMII.5 IEE802.11g Wireless LAN",
0x3886 : "Creatix CTX405 WLAN Controller / ZyAir G100 - WLAN",
0x3890 : "PRISM GT 802.11g 54Mbps Wireless Controller",
0x8130 : "NTSC/PAL Video Decoder",
0x8131 : "NTSC/PAL Video Decoder",
},
0x1266 : { 0x0001 : "NE10/100 Adapter (i82557B)",
0x1910 : "NE2000Plus (RT8029) Ethernet Adapter",
},
0x1267 : { 0x1016 : "NICCY PCI card",
0x4243 : "Satellite receiver board / MPEG2 decoder",
0x5352 : "",
0x5A4B : "",
},
0x1268 : { 0x0204 : "Tektronix IO Processor / Tektronix PCI Acquisition Interface Rev 204",
},
0x126A : { 0x269B : "SM Bus Controller",
},
0x126C : { 0x1F1F : "e-mobility 802.11b Wireless LAN PCI Card",
},
0x126F : { 0x0501 : "Mobile Multimedia Companion Chip (MMCC)",
0x0710 : "LynxEM",
0x0712 : "LynxEM+",
0x0720 : "Lynx3DM",
0x0810 : "LynxE",
0x0811 : "LynxE",
0x0820 : "Lynx3D",
0x0910 : "SILICON MOTION",
},
0x1272 : { 0x0780 : "PCIVEN_8086&DEV_1C3A",
0x1272 : "PCIVEN_8086&DEV_1C3A&SUBSYS_2ABF103C",
0x9876 : "PCIVEN_1272&DEV_0780&SUBSYS_00000008&REV_7A3&61AAA01&0&58",
},
0x1273 : { 0x0002 : "t9p17af-01",
},
0x1274 : { 0X1005 : "Serial PCI Port",
0x1274 : "multimedia audio device",
0x1371 : "AudioPCI",
0x1373 : "Sound Blaster Audio(PCI)",
0x5000 : "AudioPCI",
0x5880 : "Soundblaster (CT4750)",
0x9876 : "",
},
0x1278 : { 0x0701 : "PowerPC Node",
0x1001 : "TMB17 Motherboard",
},
0x1279 : { 0x0060 : "Efficeon Virtual Northbridge",
0x0061 : "Efficeon AGP Bridge",
0x0295 : "Virtual Northbridge",
0x0395 : "Northbridge",
0x0396 : "SDRAM Controller",
0x0397 : "BIOS scratchpad",
},
0x127E : { 0x0010 : "Videum 1000 AV Plus",
},
0x1282 : { 0x1282 : "DEV",
0x9009 : "Ethernet Adapter",
0x9100 : "",
0x9102 : "10/100 Mbps Fast Ethernet Controller",
},
0x1283 : { 0x0801 : "Audio Digital Controller",
0x673A : "IDE Controller",
0x8152 : "Advanced RISC-to-PCI Companion Chip",
0x8172 : "Ultra RISC (MIPS",
0x8211 : "ATA/ATAPI Controller",
0x8212 : "ATA 133 IDE RAID Controller",
0x8213 : "IDE Controller",
0x8330 : "Host Bridge",
0x8872 : "PCI-ISA I/O chip with SMB & Parallel Port",
0x8875 : "PCI Parallel Port",
0x8888 : "PCI to ISA Bridge",
0x8889 : "sound",
0x9876 : "PCI I/O CARD",
0xE886 : "PCI to ISA Bridge",
},
0x1285 : { 0x0100 : "Maestro-1 AudioDrive",
},
0x1287 : { 0x001E : "DVD Decoder",
0x001F : "DVD Decoder",
0x0020 : "MPEG/DVD video decoder",
},
0x1289 : { 0x1006 : "1708",
},
0x128A : { 0xF001 : "controller ethernet",
},
0x128D : { 0x0021 : "ATM Adapter",
},
0x1290 : { 0x0010 : "?",
},
0x129A : { 0x0415 : "PCI 66MHz Analyzer and 33MHz Exerciser",
0x0515 : "PCI 66MHz Analyzer and Exerciser",
0x0615 : "PCI 66MHz and PCI-X 100MHz Bus Analyzer and Exerciser",
0x0715 : "PCI 66MHz and PCI-X 133MHz Bus Analyzer and Exerciser",
0xDD10 : "Digital Parallel Input Output Device 32bit",
0xDD11 : "Digital Parallel Input Output Device 64bit",
0xDD12 : "Digital Parallel Input Output Device 64bit",
},
0x12A0 : { 0x0008 : "Allen-Bradley 1784-PKTX",
},
0x12A3 : { 0xECB8 : "V.92 Lucent Modem",
},
0x12AA : { 0x5568 : "WANic 400 series X.21 controller",
0x556C : "NAI HSSI Sniffer PCI Adapter",
},
0x12AB : { 0x3000 : "PCI",
},
0x12AD : { 0x0010 : "HERMES-S0",
0x0020 : "HERMES-PRI",
0x0080 : "HERMES-PRI/PCIX",
},
0x12AE : { 0x0001 : "ACEnic 1000 BASE-SX Ethernet adapter",
0x0002 : "Copper Gigabit Ethernet Adapter",
},
0x12B9 : { 0x00c2 : "pci simple communication controller",
0x1006 : "5610 56K FaxModem WinModem",
0x1007 : "US Robotics 56K DATA FAX WINMODEM",
0x1008 : "USR5610B (0005610-02) 56K Performance Pro Modem (PCI Internal)",
0x12b9 : "psi simple communication controller",
0x3F0 : "US Robotics 56K Fax PCI aka Model 0726",
},
0x12BA : { 0x0032 : "Hammerhead-Lite-PCI",
},
0x12C1 : { 0x9080 : "Communications Processor",
},
0x12C3 : { 0x0058 : "LAN Adapter (NE2000-compatible)",
0x5598 : "Ethernet Adapter (NE2000-compatible)",
},
0x12C4 : { 0x0001 : "",
0x0002 : "",
0x0003 : "",
0x0004 : "",
0x0005 : "BlueHeat 8 Port RS232 Serial Board",
0x0006 : "",
0x0007 : "",
0x0008 : "",
0x0009 : "",
0x000A : "",
0x000B : "",
0x000C : "",
0x000D : "",
0x000E : "",
0x000F : "",
0x0300 : "",
0x0301 : "",
0x0302 : "",
0x0303 : "",
0x0304 : "",
0x0305 : "",
0x0306 : "",
0x0307 : "",
0x0308 : "Starcom UM100 Wireless modem for WiMax ",
0x0309 : "",
0x030A : "",
0x030B : "",
},
0x12C5 : { 0x007F : "PEI Imaging Subsystem Engine",
0x0081 : "PCI Thresholding Engine",
0x0085 : "Video Simulator/Sender",
0x0086 : "Multi-scale Thresholder",
},
0x12C7 : { 0x0546 : "D120JCT-LS Card",
0x0561 : "BRI/2 Type Card (Voice Driver)",
0x0647 : "D/240JCT-T1 Card",
0x0648 : "D/300JCT-E1 Card",
0x0649 : "D/300JCT-E1 Card",
0x0651 : "MSI PCI Card",
0x0673 : "BRI/160-PCI Card",
0x0674 : "BRI/120-PCI Card",
0x0675 : "BRI/80-PCI Card",
0x0676 : "D/41JCT Card",
0x0685 : "D/480JCT-2T1 Card",
0x0687 : "D/600JCT-2E1 (75 Ohm) Card",
0x0689 : "Dialogic 2E1 - JCT series",
0x0707 : "D/320JCT (Resource Only) Card",
0x0708 : "D/160JCT (Resource Only) Card",
},
0x12CB : { 0x0027 : "studiocard",
0x002D : "agp",
0x002E : "",
0x002F : "",
0x0030 : "",
0x0031 : "",
0x0032 : "20-bit 2-in",
0x0033 : "",
0x0034 : "",
0x0035 : "",
},
0x12D1 : { 0x1001 : "MSM6246",
0x1003 : "81237",
0x140B : "EC159",
0x1412 : "09HT1407",
0x1446 : "E1800",
0x14c5 : "K4510",
0x1520 : "-e620",
0x1802 : "unknown",
0x3609 : "N/A",
},
0x12D4 : { 0x0301 : "EP1S",
},
0x12D5 : { 0x1000 : "Broadband Signal Processor",
0x1002 : "Digital Signal Processor",
},
0x12D8 : { 0x71E2 : "3 Port PCI to PCI bridge",
0x8140 : "4 Port PCI to PCI bridge",
0x8150 : "2-Port PCI to PCI Bridge",
0x8152 : "2-Port PCI-To-PCI Bridge",
0xA404 : "PCIe Packet Switch",
0xE111 : "PCI to PCIe Bridge",
0xe130 : "PCI-X Bridge",
},
0x12DB : { 0x0003 : "FoxFire II",
},
0x12DE : { 0x0200 : "Cryptoswift 200",
},
0x12DF : { 0x2102 : "Communications Controller",
0x8236 : "PCI Controller",
},
0x12E0 : { 0x0010 : "Quad UART",
0x0020 : "Quad UART",
0x0030 : "Quad UART",
},
0x12E4 : { 0x1000 : "PRI Controller",
0x1140 : "ISDN Controller",
0xB005 : "BRI Controller",
0xB006 : "BRI Controller",
},
0x12EB : { 0x0001 : "Vortex 1 Digital Audio Processor",
0x0002 : "Vortex 2 Audio Processor",
0x0003 : "Aureal Soundcard",
},
0x12EC : { 0x8139 : "0xxxx",
0x8140 : "asf",
},
0x12F2 : { 0x1002 : "Grapics Radeon X850",
0x3059 : "AC97 Enhanced Audio Controller - the 8251 controller is different",
},
0x12F8 : { 0x0002 : "s3 trio",
},
0x12FC : { 0x5cec : "IEEE 488",
},
0x1303 : { 0x0001 : "cM67 CompactPCI DSP Card",
0x0002 : "M44/cM44 DSP board",
0x0003 : "Quattro6x DSP board",
0x0004 : "Chico/ChicoPlus Data Acquisition Board",
0x0005 : "Code Hammer Jtag Debugger board",
0x0006 : "Matador DSP board",
0x0007 : "Quixote DSP board",
0x0008 : "Quadia C64x DSP",
0x0009 : "Quadia DSP Baseboard",
},
0x1307 : { 0x0001 : "",
0x0006 : "",
0x000B : "",
0x000C : "",
0x000D : "",
0x000F : "",
0x0010 : "",
0x0014 : "24 Bit Digital Input/Output Board",
0x0015 : "",
0x0016 : "",
0x0017 : "",
0x0018 : "",
0x0019 : "",
0x001A : "",
0x001B : "",
0x001C : "AR2425",
0x001D : "",
0x001E : "",
0x001F : "",
0x0020 : "",
0x0021 : "",
0x0022 : "",
0x0023 : "",
0x0024 : "",
0x0025 : "",
0x0026 : "",
0x0027 : "",
0x0028 : "24 Bit Digital Input/Output Board",
0x0029 : "",
0x002C : "PCI-INT32",
0x0033 : "",
0x0034 : "",
0x0035 : "",
0x0036 : "",
0x0037 : "",
0x004C : "",
0x004D : "",
0x0064 : "10 channels",
0x0361 : "?",
},
0x1308 : { 0x0001 : "NetCelerator Adapter",
},
0x130B : { 0x130b : "0x9876",
},
0x1310 : { 0x0003 : "CompactPCI Interface",
0x000D : "FPGA PCI Bridge",
},
0x1317 : { 0x0531 : "ADMtek AN986",
0x0981 : "FastNIC 10/100 Fast Ethernet Adapter",
0x0985 : "Linksys LNE 100TX Fast Ethernet Adapter(LNE100TX v4)",
0x1985 : "CardBus 10/100 Fast EthernetКонтроллер",
0x2850 : "HSP56 MicroModem",
0x5120 : "ADMtek ADM5120 SOC (rev: 0)",
0x7892 : "HSP56 MicroModem",
0x8201 : "802.11b Wireless PCI Card",
0x9511 : "PCI 10/100 Fast Ethernet Adapter",
0x9513 : "PCI 10/100 Fast Ethernet Adapter",
8201 : "1317",
},
0x1318 : { 0x0911 : "G-NIC II",
},
0x1319 : { 0x0801 : "PCI Card MediaForte made in singapore (driver - ct",
0x0802 : "Xwave PCI Joystick",
0x1000 : "PCI Audio",
0x1001 : "Joystick",
0x1319 : "Xwave PCI audio controller",
0x4901 : "ForteMedia PCI Audio Card",
802 : "PCI Audio",
},
0x131F : { 0x2002 : "CyberSerial 16850",
0x2011 : "Siig Inc Duet 1S(16550)+1P",
0x2012 : "Duet 1S(16850)+1P",
0x2020 : "Communication controller",
0x2030 : "SIIG Cyber Serial Dual PCI Board",
0x2042 : "Trio 1S(16850)+2P",
0x2050 : "Siig Inc CyberSerial (4-port) 16550",
0x2051 : "CyberSerial 16650",
0x2052 : "CyberSerial 16850",
0x2060 : "Trio 2S(16550)+1P",
0x2061 : "Trio 2S(16650)+1P",
0x2062 : "Trio 2S(16850)+1P",
0x9876 : "Trio 2S(16550)+1P",
},
0x1328 : { 0x2048 : "",
0x8888 : "cPEG C 3.0 DVD/MPEG2 decoder",
},
0x1332 : { 0x5410 : "PCI 32bit Bulk Memory w/DMA",
0x5415 : "PCI Battery Backed SDRAM Adapter",
0x5425 : "PCI Memory Module with Battery Backup",
0x6140 : "Memory Module",
},
0x133D : { 0x1000 : "Industrial I/O Card",
},
0x1344 : { 0x3240 : "",
0x3320 : "MT8LLN21PADF",
0x3321 : "21PAD",
0x3470 : "MT7LLN22NCNE",
0x4020 : "",
0x4030 : "",
},
0x134A : { 0x0001 : "Domex DMX 3191D PCI SCSI Controller",
0x0002 : "Domex DMX3192U/3194UP SCSI Adapter",
0x3510 : "scsi",
},
0x134D : { 0x2188 : "intel",
0x2189 : "pctel HSP56 V92 PCI Modem",
0x2486 : "V.92 MDC Modem",
0x7890 : "HSP56 MicroModem",
0x7891 : "HSP MicroModem 56",
0x7892 : "HSP56 MicroModem",
0x7893 : "HSP MicroModem 56",
0x7894 : "HSP MicroModem 56",
0x7895 : "HSP MicroModem 56",
0x7896 : "HSP MicroModem 56",
0x7897 : "HSP MicroModem 56/PCT789T",
0x9714 : "PCTEL",
0xD800 : "pctel 56k modem",
8086 : "dev",
},
0x135A : { 0x0042 : "4-port RS-232",
0x0181 : "PCI LPT and RS-232",
0x0224 : "PLX PCI Bus Logic",
0x0228 : "pq100akj9737",
},
0x135E : { 0x0EC3 : "PCIe 8 Relay Output/8 Isolated Input Board ",
0x5101 : "Route 56",
0x5102 : "RS-232 synchronous card",
0x7101 : "Single Port RS-232/422/485/520",
0x7201 : "Dual Port RS-232/422/485 Interface",
0x7202 : "Dual Port RS-232 Interface",
0x7401 : "Four Port RS-232 Interface",
0x7402 : "Four Port RS-422/485 Interface",
0x7801 : "Eight Port RS-232 Interface",
0x8001 : "Digital I/O Adapter",
},
0x1360 : { 0x0101 : "DCF77 Radio Clock",
0x0102 : "DCF77 Radio Clock",
0x0103 : "DCF77 Radio Clock",
0x0104 : "DCF77 Radio Clock",
0x0105 : "DCF77 Receiver",
0x0106 : "High Precision DCF77 Radio Clock",
0x0201 : "GPS Receiver",
0x0202 : "GPS Receiver",
0x0203 : "GPS Receiver",
0x0204 : "GPS Receiver",
0x0205 : "GPS Receiver",
0x0206 : "GPS receiver",
0x0301 : "IRIG Timecode Reader",
0x0302 : "IRIG Timecode Reader",
0x0303 : "IRIG Timecode Reader",
0x0304 : "IRIG Timecode Receiver",
0x0305 : "IRIG Timecode Reader",
0x0306 : "IRIG Timecode Reader",
0x0501 : "PTP/IEEE1588 Slave Card",
0x0601 : "Free Running Clock",
},
0x1365 : { 0x9050 : "",
},
0x1375 : { 0x2571 : "NA",
},
0x137A : { 0x0001 : "",
0x0003 : "PCI-424 Original",
0x0004 : "PCI-424 X",
0x0005 : "PCIe-424",
},
0x1382 : { 0x0001 : "Sek'D ARC88 professional soundcard",
0x2009 : "SEK'D Prodif 96 Pro - professional audio card",
0x2048 : "Prodif Plus sound card",
0x2088 : "8-in",
},
0x1385 : { 0x4100 : "802.11b Wireless Adapter",
0x4105 : "",
0x620A : "Toshiba",
0x622A : "",
0x630A : "",
0x8169 : "Gigabit Ethernet Adapter",
0xF311 : "Fast Ethernet Adapter",
0xF312 : "",
},
0x1387 : { 0x4640 : "sl240",
0x5310 : "SCRAMNet GT200",
},
0x1389 : { 0x0001 : "Intelligent fieldbus Adapter",
0x0104 : "PCI-CANIO adapter",
},
0x138A : { 0x0001 : "0001",
0x0005 : "0008",
0x0006 : "0006",
0x0007 : "0007",
0x0009 : "0008",
0x0011 : "11",
0x0018 : "Biometric Devices",
0x003C : "0008",
0x003D : "0104",
0x11 : "VFS5011",
},
0x1393 : { 0x1010 : "",
0x1020 : "",
0x1022 : "unknown",
0x1040 : "Smartio",
0x1041 : "",
0x1042 : "",
0x1140 : "",
0x1141 : "",
0x1320 : "Industio",
0x1321 : "",
0x1340 : "UniversalPCI board",
0x1401 : "",
0x1680 : "Smartio",
0x1681 : "CP-168U Smart Serial Board",
0x2040 : "Intellio",
0x2180 : "Intellio Turbo PCI",
0x2210 : "---",
0x2240 : "---",
0x3200 : "Intellio Turbo PCI",
0x5020 : "",
0x6800 : "dvr capture card",
},
0x1394 : { 0x0001 : "Gigabit Ethernet Adapter",
},
0x1397 : { 0x0B4D : "ISDN HDLC FIFO Controller",
0x2BD0 : "ISDN HDLC FIFO Controller",
0x8B4D : "ISDN HDLC FIFO Controller",
0xB000 : "HCF-PCI card",
0xB006 : "HCF-PCI card",
0xB007 : "HCF-PCI card",
0xB008 : "usb webcam",
0xB009 : "HCF-PCI card",
0xB00A : "HCF-PCI card",
0xB00B : "HCF-PCI card",
0xB00C : "HCF-PCI card",
0xB100 : "HCF-PCI card",
},
0x139A : { 0x0007 : "Alacritech iSCSI Controller",
},
0x13A3 : { 0x0005 : "Security Processor",
0x0006 : "Public Key Processor",
0x0007 : "Security Processor",
0x0012 : "Security Processor",
0x0014 : "Security Processor",
0x0015 : "Security Processor",
0x0017 : "Security Processor",
0x0018 : "Security Processor",
0x001d : "Cryptographic Processor",
0x0020 : "Cryptographic Processor",
0x0026 : "Security Processor",
0x16 : "Security Processor",
},
0x13A7 : { 0x6240 : "BSRV2-301A",
},
0x13A8 : { 0x0152 : "Dual UART",
0x0154 : "Four Channel PCI Bus UART",
0x0158 : "Eight Channel PCI Bus UART (5V)",
},
0x13B6 : { 0x13b6 : "sguiu",
},
0x13C0 : { 0x0010 : "single port multiprotocol serial adapter",
0x0020 : "low speed single port multiprotocol serial adapter",
0x0030 : "4 port multiprotocol serial adapter",
0x0070 : "single port multiprotocol serial adapter",
0x0080 : "4 port multiprotocol serial adapter",
0x0090 : "one port asynchronous serial adapter",
0x00a0 : "2 port multiprotocol serial adapter",
0x0210 : "single port multiprotocol serial adapter",
},
0x13C1 : { 0x1000 : "ATA-RAID Controller",
0x1001 : "ATA-133 Storage Controller",
0x1002 : "SATA/PATA Storage Controller",
0x1003 : "SATA2 Raid Controller",
0x1004 : "PCI-Express SATA2 Raid Controller",
0x1005 : "PCI-Express SATA2/SAS Raid Controller",
0x1010 : "PCI-Express2 SAS2/SATA2 Raid Controller",
},
0x13C7 : { 0x0ADC : "Multi-Function Analogue/Digital IO card",
0x0B10 : "Parallel I/O Card",
0x0D10 : "Digital I/O Card",
0x5744 : "Watchdog Card",
},
0x13D0 : { 0x2103 : "B2C2 Sky2PC Core Chip sky star 2 <technisat>",
0x2200 : "",
},
0x13D1 : { 0xAB02 : "",
0xAB03 : "",
0xAB06 : "FE2000VX",
0xAB08 : "SMC8035TX",
},
0x13D7 : { 0x0205 : "toshiba",
0x8086 : "toshiba",
},
0x13D8 : { 0x1000 : "XaQti 1000Mbit/sec Gbit Ethernet Controller",
},
0x13DF : { 0x0001 : "Modem",
},
0x13EA : { 0x3131 : "BoSS Bit Synchronous HDLC Controller",
0x3134 : "Chateau Channelized T1/E1/HDLC Controller",
},
0x13F0 : { 0x0200 : "IP100A Integrated 10/100 Ethernet MAC + PHY",
0x0201 : "Fast Ehternet Adapter",
0x0300 : "Network Adapter",
0x1021 : "Tamarack 9021A Gigabit Ethernet adapter",
0x1023 : "Gigabit Ethernet Controllera",
0x13F0 : "ST201 Fast Ethernet ��� � �'�",
},
0x13F1 : { 0x0028 : "MCP67 High Definition Audio",
},
0x13F6 : { 0211 : "serlio",
0x0011 : "sound card",
0x0100 : "PCI",
0x0101 : "PCI Audio Device",
0x0111 : "C-Media Audio Controller",
0x0112 : "PCI Audio Chip",
0x0191 : "CMI 8738 8CH Sound Card",
0x0211 : " Driver controller pci simple comunications - PCtel HSP56 Micro Modem Driver ",
0x0300 : "pci audio driver",
0x111 : "C-Media Audio Controller",
0x8788 : "C-Media Oxygen HD",
0x9876 : "C-Media Audio Controller",
0x9891 : "C-Media Audio Controller",
},
0x13FD : { 0x160E : "SATA/150 device to USB 2.0",
0x161F : "s",
0x1840 : "SATA/150 device to USB 2.0 Host interface (http://www.initio.com/Html/inic-1608.html)",
},
0x13FE : { 0x1240 : "PS2134CE-0",
0x1600 : "PCI-1610CU/9-AE",
0x1680 : "PCI-1680U-A",
0x16FF : "PCI-1610CU/9-AE",
0x1713 : "PCI-1713",
0x1723 : "PCI-1723",
0x1724 : "PCI-1723",
0x1755 : "PCI-1755",
0x1760 : "amcc pci matchmaker s5920q",
0x1761 : "PCI-1751",
0x1762 : "PCI-1762",
0x1a00 : "0x03",
0x3730 : "PCM-3730I",
},
0x1400 : { 0x0001 : "",
0x0003 : "",
0x0004 : "030000",
0x1401 : "hd 2600xt",
},
0x1402 : { 0x2E00 : "Multifunction Data Aquistion card",
0x4610 : "Multi-IO board (16x 16bit ADC",
0x4650 : "Multi-IO board (16x 16bit ADC",
},
0x1407 : { 0x0100 : "Lava Dual Serial 550 PCI",
0x0101 : "Lava Quattro PCI A/B",
0x0102 : "Lava Quattro PCI C/D",
0x0110 : "Lava DSerial PCI Port A",
0x0111 : "Lava DSerial PCI Port B",
0x0180 : "Lava Octopus PCI Ports 1-4",
0x0181 : "Lava Octopus PCI Ports 5-8",
0x0200 : "LavaPort Dual-650 PCI",
0x0201 : "LavaPort Quad-650 PCI A/B",
0x0202 : "LavaPort Quad-650 PCI C/D",
0x0220 : "LavaPort Quad-650 PCI A/B",
0x0221 : "LavaPort Quad-650 PCI C/D",
0x0400 : "Lava 8255 PIO PCI",
0x0500 : "Lava Single Serial 550 PCI",
0x0510 : "Lava SP Serial 550 PCI",
0x0511 : "Lava SP BIDIR Parallel PCI",
0x0520 : "Lava RS422 SS-PCI",
0x0600 : "LavaPort 650 PCI",
0x0A00 : "COM Port Accelerator",
0x120 : "Lava Quattro 550 PCI A/B",
0x121 : "Lava Quattro 550 PCI C/D",
0x520 : "s",
0x8000 : "Lava Parallel",
0x8001 : "Lava Dual Parallel port A",
0x8002 : "Lava Dual Parallel port A",
0x8003 : "Lava Dual Parallel port B",
0x8800 : "BOCA Research IOPPAR",
},
0x1409 : { 0x7168 : "40371409",
0x7268 : "PCI / ISA IEEE1284 ECP/EPP/SPP/BPP Signal Chips So",
7268 : "PCI / ISA IEEE1284 ECP/EPP/SPP/BPP PAR4008A",
},
0x140B : { 0x0610 : "",
0x615 : "Na",
0x682 : "NA",
},
0x1412 : { 0x1712 : "ICE1712",
0x1724 : "VT1723",
},
0x1415 : { 0x8401 : "PCI Interface to local bus",
0x8403 : "PCI Parallel Card",
0x9500 : "Quad UART (disabled)",
0x9501 : "Quad UART",
0x9505 : "Dual UART",
0x950A : "Dual PCI UARTS",
0x950B : "Integrated High Performance UART",
0x9510 : "PCI Interface (disabled)",
0x9511 : "PCI Interface to 8-bit local bus",
0x9512 : "PCI Interface to 32-bit bus",
0x9513 : "Parallel Port",
0x9521 : "Dual UART",
0x9523 : "Integrated Parallel Port",
0xc110 : "Parallel PCI Express Card (Manhattan 158176)",
0xc158 : "2 native UARTs (function 0)",
0xc15d : "2 native UARTs (function 1)",
0xc208 : "Quad UARTs",
0xc20d : "Quad UARTs (function 1)",
0xc308 : "Octo UARTs",
0xc30d : "Octo UARTs (function 1)",
},
0x141F : { 0x6181 : "MPEG decoder",
},
0x1425 : { 0x0030 : "T310 10GbE Single Port Adapter",
0x31 : "T320 10GbE Dual Port Adapter",
0x32 : "T302 1GbE Dual Port Adapter",
0x33 : "T304 1GbE Quad Port Adapter",
0x34 : "B320 10GbE Dual Port Adapter",
0x35 : "S310-CR 10GbE Single Port Adapter",
0x36 : "S320-LP-CR 10GbE Dual Port Adapter",
0x37 : "N320-G2-CR 10GbE Dual Port Adapter",
0x4401 : "T420-CR Unified Wire Ethernet Controller",
0x4402 : "T422-CR Unified Wire Ethernet Controller",
0x4403 : "T440-CR Unified Wire Ethernet Controller",
0x4404 : "T420-BCH Unified Wire Ethernet Controller",
0x4405 : "T440-BCH Unified Wire Ethernet Controller",
0x4406 : "T440-CH Unified Wire Ethernet Controller",
0x4407 : "T420-SO Unified Wire Ethernet Controller",
0x4408 : "T420-CX Unified Wire Ethernet Controller",
0x4409 : "T420-BT Unified Wire Ethernet Controller",
0x440a : "T404-BT Unified Wire Ethernet Controller",
0x440d : "T480 Unified Wire Ethernet Controller",
0x440e : "T440-LP-CR Unified Wire Ethernet Controller",
0x7145 : "N/A",
},
0x1435 : { 0x0531 : "DELETE",
0x6020 : "SPM6020",
0x6030 : "SPM6030",
0x6420 : "SPM186420",
0x6430 : "SPM176430",
0x7520 : "DM7520",
0x7540 : "SDM7540",
},
0x1448 : { 0x0001 : "Audio Editing",
},
0x144A : { 0x348A : "Low-profile High-Performance IEEE488 GPIB Interface Card for PCI Bus",
0x7230 : "",
0x7248 : "PLX PCI9052",
0x7250 : "PLX PCI9052",
0x7256 : "PCI-7256 16-CH Latching Relay & 16-CH Isolated Digital Input Card",
0x7296 : "96-ch digital I/O card",
0x7432 : "",
0x7433 : "64-ch digital Input card",
0x7434 : "",
0x7841 : "SJA 1000- baseddual port CAN bus card",
0x8133 : "Dell Wireless 5720 VZW Mobile Broadband Card",
0x8554 : "",
0x9111 : "",
0x9113 : "",
0x9114 : "",
},
0x144B : { 0x0601 : "",
},
0x1458 : { 0x1458 : "microsoft",
0x5000 : "GA-X48T-DQ6",
},
0x145F : { 0x0001 : "Multi-axis Motion Controller",
0x0002 : "Multi-axis Motion Controller",
},
0x1462 : { 0x00C1 : "NX6800-TD256E",
0x4720 : "Audio controller",
0x5071 : "Audio controller",
0x5964 : "RADEON 9250/9200 series AGP",
0x7120 : "",
0x7960 : "MCP2T",
},
0x1471 : { 0x0188 : "ADSL PCI",
},
0x148C : { 0x4011 : "RADEON 9000 PRO EVIL COMMANDO",
0x4152 : "0x2079",
},
0x148D : { 0x1003 : "Creative ModemBlaster V.90 PCI DI5655",
},
0x148F : { 0x1000 : "Ralink Motorola BC4 Bluetooth 3.0+HS Adapter",
0x148f : "TP-LINK 7200ND",
0x2000 : "Ralink Motorola BC8 Bluetooth 3.0 + HS Adapter",
0x2070 : "802.11 g WLAN",
0x2573 : "802.11 bg",
0x2870 : "802.11 n WLAN",
0x3000 : "802.11n + Bluetooth 3.0",
0x3070 : "FreeWifiLink D3-10000N",
0x3572 : "Ralink 3572",
0x5370 : "802.11n USB Wireless LAN Card",
0x9021 : "Netopia USB b/g Adapter (black)",
},
0x1491 : { 0x0020 : "USB Fingerprint Scanner Model FS80",
0x0021 : "USB Fingerprint Scanner Model FS80",
},
0x14A9 : { 0xad1f : "1",
},
0x14B1 : { 0x1033 : "RH56D-PCI",
0x2F30 : "zyxel omni 56k CI lus rev.",
},
0x14B3 : { 0x0000 : "DSL NIC",
},
0x14B5 : { 0x0200 : "",
0x0300 : "",
0x0400 : "",
0x0600 : "",
0x0800 : "DSP-Board",
0x0900 : "DSP-Board",
0x0A00 : "DSP-Board",
0x0B00 : "DSP-Board",
},
0x14B7 : { 0x0001 : "pci9052",
},
0x14B9 : { 0x0001 : "werwerwerwe",
0x0340 : "Cisco Systems 340 PCI Wireless LAN Adptr",
0x2500 : "Wireless PCI LAN Adapter",
0x3100 : "Wireless PCI LAN Adapter",
0x3101 : "Wireless PCI LAN Adapter",
0x3500 : "Wireless PCI LAN Adapter",
0x4500 : "Wireless PCI LAN Adapter",
0x4800 : "Wireless PCI LAN Adapter",
0xA504 : "Cisco Aironet 350 Series Mini-PCI (MPI350)",
0xA506 : "802.11b/g wireless adapter",
},
0x14C1 : { 0x8043 : "MyriNet",
},
0x14C8 : { 0x0003 : "0",
},
0x14CD : { 0x03 : "0x0200",
},
0x14CF : { 0x2920 : "Serial I/O Controller aka FPMC-DFLEX64",
},
0x14D4 : { 0x0400 : "Interface chip",
},
0x14D9 : { 0x0010 : "Sturgeon HyperTransport-PCI Bridge",
},
0x14DB : { 0x2100 : "download drivers",
0x2101 : "",
0x2102 : "",
0x2110 : "OX16PCI952",
0x2111 : "",
0x2112 : "",
0x2120 : "0701 Parallel Port device",
0x2121 : "Avlab Technology PCI IO 2P",
0x2130 : "2 Port PCI Serial Card",
0x2131 : "pci serial port",
0x2132 : "",
0x2140 : "",
0x2141 : "",
0x2142 : "",
0x2144 : "",
0x2145 : "",
0x2146 : "",
0x2150 : "",
0x2151 : "",
0x2152 : "",
0x2160 : "",
0x2161 : "",
0x2162 : "",
0x2180 : "VEN_14DB&DEV_2180&SUBSYS_218014DB&REV_00",
0x2181 : "Avlab Technology Inc",
0x2182 : "Avlab Technology Inc",
},
0x14DC : { 0x0000 : "",
0x0001 : "4-port high speed RS-232",
0x0002 : "8-port high speed RS-232",
0x0003 : "2-port high speed RS-232",
0x0004 : "2-port high speed RS-422/485",
0x0005 : "2-port high speed RS-232 and RS-422/485",
0x0006 : "16-channel analog input (with timers)",
0x0007 : "16-chan 12-bit analog output (w/ timers)",
0x0008 : "4-chan 16-bit analog output (w/ timers)",
0x0009 : "24-channel digital I/O",
0x000A : "72-channel digital I/O",
0x000B : "48-channel digital I/O (w/ 6 timers)",
0x000C : "16-channel reed relay output",
},
0x14E4 : { 0x0038 : "100G packet processor ",
0x0102 : "Intel (R)",
0x0318 : "n/a",
0x034F : "???",
0x04B5 : "Broadcom 54bg Wireless",
0x0732 : "2x40G/8x10G MAC Aggregation Switch with 80G Uplink",
0x0800 : "Sentry5 Chipcommon I/O Controller",
0x0804 : "Sentry5 PCI Bridge",
0x0805 : "Sentry5 MIPS32 CPU",
0x0806 : "Sentry5 Ethernet Controller",
0x080B : "Sentry5 Crypto Accelerator",
0x080F : "Sentry5 DDR/SDR RAM Controller",
0x0811 : "Sentry5 External Interface",
0x0816 : "Sentry5 MIPS32 CPU",
0x1234 : "networkcontroller",
0x1361 : "Ethernet",
0x14E4 : "802.11b/g Wireless Lan Controller",
0x1600 : "NetXtreme BCM5752 Gigabit Ethernet PCI Express",
0x1601 : "NetXtreme Desktop/Mobile",
0x1610 : "Broadcom BCN70010 Video Decoder",
0x1612 : "Crystal HD Video Decoder",
0x1615 : "Broadcom Crystal HD Video Decoder",
0x161F : "AVC/VC-1/MPEG PCI Express HD Decoder Chipset for Netbooks/Nettops",
0x1639 : "NetXtreme Gigabit Ethernet II",
0x163B : "Broadcom NetXtreme II BCM5706/5708/5709/5716 Driver",
0x1644 : "ven_1102dev_0004",
0x1645 : "broadtcomBCM5701 Gigabit EthernetASD",
0x1646 : "NetXtreme Gigabit Ethernet",
0x1647 : "NetXtreme Gigabit Ethernet",
0x1648 : "NetXtreme Dual Gigabit Adapter",
0x164C : "Broadcom NetXtreme II Gigabit Ethernet Adapter",
0x164D : "NetXtreme Fast Ethernet Controller",
0x1650 : "Broadcom PCIe 10Gb Network Controller ",
0x1653 : "Broadcom NetXtreme Gigabit Ethernet",
0x1654 : "NetXtreme Gigabit Ethernet",
0x1658 : "NtXtreme Gigabit Ethernet",
0x1659 : "NetXtreme Gigabit Ethernet PCI Express",
0x165A : "Broadcom NetXtreme BCM5722 Gigabit",
0x165D : "Broadcom NetXtreme Gigabit Ethernet",
0x165E : "NetXtreme Gigabit Ethernet",
0x165F : "Broadcom NetXtreme 5720 Gigabit Ethernet",
0x166a : "Broadcom NetXtreme Gigabit Ethernet 5780",
0x166B : "NetXtreme Gigabit Ethernet",
0x166D : "NetXtreme Ethernet 100kB",
0x166E : "NetXtreme Gigabit Ethernet",
0x167 : "NetXtreme Fast Ethernet Controller",
0x1672 : "NetXtreme Gigabit Ethernet",
0x1673 : "NetXtreme Gigabit Ethernet",
0x1674 : "57XX Series Broadcom Driver X86/X64",
0x1676 : "NetXtreme Gigabit Ethernet",
0x1677 : "NetXtreme Desktop/Mobile",
0x1677 : "Broadcom NetExtreme Gigabit Ethernet",
0x167A : "Broadcom NetXtreme Gigabit Ethernet Controller",
0x167B : "NetXtreme Gigabit Ethernet",
0x167C : "NetXtreme Gigabit Ethernet",
0x167d : "Broadcom NetXtreme Gigabit Ethernet",
0x167E : "vierkant",
0x1680 : "NetXtreme Desktop/Mobile",
0x1681 : "Broadcom 57XX Gigabit Integrated Controller ",
0x1684 : "Broadcom NetXtreme Gigabit Ethernet",
0x1690 : "NexTreme Desktop/Mobile",
0x1691 : "Broadcom BCM57788 LOM ",
0x1691 : "Broadcom NetLink (TM) Gigabit Ethernet",
0x1692 : "NetLink",
0x1693 : "Ethernet Controller Broadcom Netlink Gigabit",
0x1696 : "Broadcom NetXtreme Gigabit Ethernet ",
0x1698 : "NetLink-FOR DELL LAPTOP AND MAYBE OTHERS",
0x169A : "Broadcom Netlink (TM) gigabit ethernet Driver",
0x169B : "NetXtreme Gigabit Ethernet",
0x169C : "Broadcom NetLink (TM) Gigabit Ethernet",
0x169D : " BCM5789",
0x169E : "NetXtreme Gigabit Ethernet PCI Express",
0x16A6 : "Gigabit Ethernet",
0x16A7 : "Gigabit Ethernet",
0x16A8 : "NetXtreme Gigabit Ethernet",
0x16AA : "BroadCom NetExtreme II Server",
0x16B1 : "BCM57781",
0x16B5 : "Broadcom NetLink Gigabit Ethernet",
0x16BE : "CardReader Broadcom 1.0.0.221",
0x16BF : "CardReader Broadcom 1.0.0.221",
0x16C6 : "NetXtreme Gigabit Ethernet",
0x16C7 : "DELL Wireless 1390 WLAN MiniCard",
0x16DD : "NetXtreme Gigabit Ethernet",
0x16f7 : "NetXtreme BCM5753 Gigabit PCI Express",
0x16FD : "NetXtreme Gigabit Ethernet PciXpress",
0x16FE : "NetXtreme Gigabit Ethernet",
0x170C : "Broadcom 440x 10/100 Integrated Controller",
0x170D : "NetXtreme",
0x170E : "NetXtreme 100Base-TX",
0x1713 : "Broadcom NetLink (TM) Fast Ethernet",
0x333 : "16p 1G (PHY)",
0x3352 : "BCM3352 QAMLink Single-Chip 4-Line VoIP",
0x3360 : "Advanced PHY Broadband Gateway Cable Modem",
0x4211 : "10Mb/s NIC",
0x4212 : "56k Modem",
0x4301 : "Dell Truemobile 1180 802.11g MiniPCI",
0x4303 : "BCM4301 802.11b802.11b Wireless LAN Controller",
0x4305 : "V.90 56k Modem",
0x4306 : "Unknown device 4306 (rev 02)",
0x4307 : "802.11b Wireless LAN Controller",
0x4310 : "BCM4301 802.11bChipcommon I/O Controller",
0x4311 : "Wireless LAN BroadCom",
0x4312 : "broadcom wireless 1490 (dell)",
0x4313 : "wireless network card",
0x4315 : "Broadcom Wireless b/g (Tested Drivers)",
0x4318 : "Broadcom 802.11b/g",
0x4320 : "802.11B/G Wireless Lan Controller Revision 3",
0x4321 : "802.11a Wireless LAN Controller",
0x4322 : "UART",
0x4323 : "V.90 56k Modem",
0x4324 : "802.11a/b/g Wireless LAN",
0x4325 : "802.11b/g Wireless LAN Controller",
0x4326 : "Chipcommon I/O Controller?",
0x4328 : "Broadcom BCM43xx 1.0 (5.10.91.27)",
0x4329 : "Broadcom 802.11n Network Adapter",
0x432B : "Broadcom Wireless LAN Driver ",
0x4353 : "Broadcom Half Mini PCI Express Wifi card / DL1520",
0x4357 : "Broadcom WiFi 802.11b/g/n",
0x4358 : "Broadcom 802.11n WLAN module",
0x4359 : "Half-mini wireless-N card DW1530",
0x4365 : "Broadcom 43142 Wireless LAN Adapter",
0x4401 : "10/100 Integrated Ethernet Controller",
0x4402 : "10/100 Integrated Ethernet Controller",
0x4403 : "V.90 56k Modem",
0x4410 : "iLine32 HomePNA 2.0",
0x4411 : "V.90 56k Modem",
0x4412 : "10/100BaseT Ethernet",
0x4430 : "CardBus iLine32 HomePNA 2.0",
0x4432 : "CardBus 10/100BaseT Ethernet",
0x4610 : "Sentry5 PCI to SB Bridge",
0x4611 : "Sentry5 iLine32 HomePNA 1.0",
0x4612 : "Sentry5 V.90 56k Modem",
0x4613 : "Sentry5 Ethernet Controller",
0x4614 : "Sentry5 External Interface",
0x4615 : "Sentry5 USB Controller",
0x4704 : "Sentry5 PCI to SB Bridge",
0x4708 : "Crypto Accelerator",
0x4710 : "Sentry5 PCI to SB Bridge",
0x4711 : "Sentry5 iLine32 HomePNA 2.0",
0x4712 : "Sentry5 V.92 56k modem",
0x4713 : "Sentry5 Ethernet Controller",
0x4714 : "Sentry5 External Interface",
0x4715 : "Sentry5 USB Controller",
0x4716 : "Sentry5 USB Host Controller",
0x4717 : "Sentry5 USB Device Controller",
0x4718 : "Sentry5 Crypto Accelerator",
0x4720 : "MIPS CPU",
0x4726 : "01",
0x4727 : "Broadcom 802.11g Network Adapter BCM4313",
0x4728 : "01",
0x5334 : "16P 1G (PHY)",
0x5365 : "Sentry5 PCI to SB Bridge",
0x5600 : "StrataSwitch 24+2 Ethernet Switch Controller",
0x5605 : "StrataSwitch 24+2 Ethernet Switch Controller",
0x5615 : "StrataSwitch 24+2 Ethernet Switch Controller",
0x5625 : "StrataSwitch 24+2 Ethernet Switch Controller",
0x5645 : "StrataSwitch 24+2 Ethernet Switch Controller",
0x5670 : "8-Port 10GE Ethernet Switch Fabric",
0x5680 : "G-Switch 8-Port Gigabit Ethernet Switch Controller",
0x5690 : "12-port Multi-Layer Gigabit Ethernet Switch",
0x5691 : "GE/10GE 8+2 Gigabit Ethernet Switch Controller",
0x5802 : "The BCM5802 Security Processor integrates Broadcoms IPSec engine (DES",
0x5805 : "The BCM5805 Security Processor integrates a high-performance IPSec engine (DES",
0x5820 : "Crypto Accelerator",
0x5821 : "Crypto Accelerator",
0x5822 : "Crypto Accelerator",
0x5823 : "Crypto Accelerator",
0x5824 : "Crypto Accelerator",
0x5825 : "BCM5825",
0x5840 : "Crypto Accelerator",
0x5841 : "Crypto Accelerator",
0x5850 : "Crypto Accelerator",
0x7321 : "network card integrated",
0x7411 : "High Definition Video/Audio Decoder",
0x7865 : "Wireless-N WLAN",
0x8010 : "Next generation router SOC with gigabit switch",
0x8011 : "Next generation router SOC with gigabit switch",
0x8012 : "Next generation router SOC with gigabit switch",
0x8016 : "Next generation router SOC with gigabit switch with RGMII/SDIO",
0x8018 : "Next generation router SOC with gigabit switch with RGMII/SDIO",
0x8019 : "Next generation router SOC with gigabit switch without RGMII/SDIO",
0x8022 : "Next generation router SOC with gigabit switch with RGMII/SDIO",
0x8023 : "Next generation router SOC with gigabit switch with SATA instead of RGMII/SDIO",
0x8025 : "Next generation router SOC with gigabit switch with RGMII/SDIO",
0x8334 : "24 1G",
0x8342 : "8 1G (PHY)",
0x8344 : " 24P 1G +4P 1G (PHY)",
0x8346 : "24P 1G +4P 1G/10G (PHY)",
0x8393 : "14P (1G",
0x8394 : "10P 1G + 4x1/2.5/5/10G (no PHY) ",
0x9867 : "900000000",
0x9876 : "0x14E4",
0xA8D6 : "Broadcom 802.11n WLAN chip",
0xB150 : "Hurricane2 (Lightly Managed) 24P 1G +4P 1G/10G (PHY)",
0xb152 : "24P 1G (PHY)",
0xB340 : "48-port multi-layer switch with embedded CPU",
0xB450 : "100G Multi-layer Ethernet Switch",
0xB640 : "260Gbps Extensible Switch with 100GE",
0xB845 : "640G Multi-layer Ethernet Switch",
0xB850 : "1.28T I/O Multi-layer Ethernet Switch",
0x4311 : "subsys",
},
0x14EA : { 0xAB06 : "XFNW-3603-T",
},
0x14EB : { 0x0020 : "PCI to S5U13xxxB00B Bridge Adapter",
0x0C01 : "Embedded Memory Display Controller",
},
0x14EC : { 0x16BE : "1.0.0.222_W7x86_A",
},
0x14F1 : { 0x0F00 : "cx11252-11",
0x0F30 : "0x14F1",
0x1031 : "332",
0x1033 : "RH56D",
0x1033 : "RH56D",
0x1035 : "R6795-11",
0x1036 : "Conexant RH56D/SP-PCI",
0x1056 : "4-1b359d48-0-10f06",
0x1059 : "DI15630-5",
0x10B4 : "Conextant HFC",
0x10B6 : "unknown",
0x1416 : "",
0x1456 : "1456",
0x14F1 : "0x14F1",
0x1611 : "?",
0x1612 : "8",
0x2013 : "0x56",
0x2400 : "unknown",
0x2702 : "cx11252-11",
0x2710 : "",
0x2740 : "CC_0780",
0x2B10 : "0x14F1",
0x2BFA : "0x0000ffff",
0x2C06 : "136",
0x2F00 : "00101767",
0x2f01 : "0x0780",
0x2F10 : "USR90-12",
0x2F20 : "CX11256",
0x2F30 : "CX11252-41z",
0x2F30 : "01",
0x2F40 : "200014F1",
0x2F50 : "99269",
0x2F52 : "C0220001",
0x2F81 : " ",
0x2F82 : "cx9510-11z",
0x5045 : "4.0.3.1",
0x5045 : "14f12f30",
0x5045 : "14e4",
0x5045 : "PCIVEN_14F1&DEV_5047",
0x5047 : "Not sure",
0x5051 : "4.0.1.6",
0x5051 : "DG31PR",
0x5051 : "CX20561",
0x5066 : "Cx20561",
0x5069 : "20585",
0x506C : "0x506C",
0x506E : "001",
0x50A1 : "CX20641/CX20651",
0x50A2 : "Conexant CX20642",
0x5B7A : "Belived to be a CX23416",
0x8800 : "Conexant CX23881",
0x8800 : "0x14F1",
0x8801 : "CX23880",
0x8802 : "CX2388x",
0x8811 : "CX2388x",
0x8852 : "cx23885",
0x8880 : "CX23888",
0x9876 : "PCIVEN_14F1&DEV_2F20&SUBSYS_200F14F1&REV_004&1AF",
0x27d8 : "A62516F3",
},
0x14F2 : { 0x0001 : "",
0x0002 : "",
0x0120 : "win7_rtm.090713-1255",
0x0121 : "",
0x0122 : "unknown",
0x0123 : "6.1.7600.16385",
0x0124 : "3103",
},
0x14F5 : { 0x2F00 : "x",
},
0x14FD : { 0x0001 : "H260u printer server for HP Printer",
},
0x1507 : { 0x0001 : "",
0x0002 : "",
0x0003 : "",
0x0100 : "",
0x0431 : "",
0x4801 : "",
0x4802 : "",
0x4803 : "",
0x4806 : "",
},
0x1516 : { 0x0800 : "10/100 Mbps Fast Ethernet Controller",
0x0803 : "PCI Ethernet controller",
0x0891 : "10/100/1000 Mbps Gigabit Ethernet Controller",
},
0x1519 : { 0x0020 : "HSIC Device",
0x2004 : "PCI Interface bus",
},
0x151A : { 0x1002 : "4341",
0x1004 : "",
0x1008 : "",
},
0x151B : { 0x9080 : "combox cb 300a",
},
0x151D : { 0x9876 : "?",
},
0x151F : { 0x0001 : "TOPIC FM-56PCI-TP",
0x0568 : "56k Internal Data Fax Voice Modem",
},
0x1522 : { 0x0100 : "PCI Interface Chip",
},
0x1523 : { 0x8 : "Content Addressable Memory",
},
0x1524 : { 0x0751 : "pci",
0x0100 : "ENE CIR Receiver",
0x0510 : "PCI Memory Card Reader Controller",
0x0530 : "Memory Stick Card Reader",
0x0550 : "Secure Digital Card Reader",
0x0551 : "ven1524&dev_0551&SUBSYS_009F1025&REV_01",
0x0555 : "ven1524&dev_0551&SUBSYS_009F1025&REV_01",
0x0610 : "PCI Smart Card Reader Controller",
0x0730 : "CardBus Controller",
0x100 : "ENE CIR Receiver",
0x1025 : "PCIVEN_127a&DEV_1025&SUBSYS_1025123A&REV_014&1351887D&0&58F0",
0x1211 : "CardBus Controller",
0x1225 : "CardBus Controller",
0x1410 : "CardBus Controller",
0x1411 : "pci device",
0x1412 : "Cardbus Controller",
0x1420 : "CardBus Controller",
0x1421 : "CardBus Controller",
0x1422 : "CardBus Controller",
0x510 : "PCI Memory Card Reader Controller",
0x551 : "ven1524&dev_0551&SUBSYS_009F1025&REV_01",
0x9876 : "1941",
0xFC10 : "pci device",
},
0x152D : { 0x2329 : "J micron JM20329",
},
0x152E : { 0x2507 : "0",
},
0x1538 : { 0x0301 : "Tekram DC200 PATA100 RAID Controller",
0x0303 : "ARS0304S PATA133 RAID5",
},
0x153B : { 0x1115 : "IC Ensemble Inc ICE1712 Envy24 Multichannel Audio Controller",
0x1143 : "Philips Semiconductors SAA7134HL Multimedia Capture Device",
0x6003 : "CrystalClear SoundFusion PCI Audio Accel",
},
0x153F : { 0xdead : "xx12345",
},
0x1540 : { 0x9524 : "PAL/SECAM TV card w/ FM1216ME MK3 tuner (+FM radio)",
},
0x1543 : { 0x1052 : "Modem Intel 537EP (Chipset KAIOMY)",
0x3052 : "Modem Intel 537EP (Chipset KAIOMY)",
0x3155 : "Modem Device on High Definition Audio Bus",
},
0x1549 : { 0x80FF : "PCI/ISA Bus Bridge",
},
0x154A : { 0x9016 : "USB DVB-T Device AF9015",
0x9876 : "USB DVB-T Device CE950081",
},
0x154B : { 0x3038 : "USB",
},
0x1555 : { 0x0002 : "Easylon PCI Bus Interface",
},
0x1556 : { 0x5555 : "an cpci application",
},
0x1558 : { 0x1558 : "gtx 670mx GPU",
},
0x155E : { 0x0020 : "Multi Function Card Version 3",
},
0x1562 : { 0x0001 : "LA-41x3",
0x0002 : "LA-5030",
0x0003 : "LA-5033",
},
0x156A : { 0x5000 : "Wideband Advanced Signal Processor",
0x5100 : "High Data Rate Radio",
},
0x1571 : { 0xA001 : "GHB",
0xA002 : "ARCnet",
0xA003 : "ARCnet",
0xA004 : "ARCnet",
0xA005 : "ARCnet",
0xA006 : "ARCnet",
0xA007 : "ARCnet",
0xA008 : "ARCnet",
0xA009 : "5 Mbit ARCnet",
0xA00A : "5 Mbit ARCnet",
0xA00B : "5 Mbit ARCnet",
0xA00C : "5 Mbit ARCnet",
0xA00D : "5 Mbit ARCnet",
0xA00E : "ARCNET",
0xA201 : "10 Mbit ARCnet",
0xA202 : "10 Mbit ARCnet",
0xA203 : "10 Mbit ARCnet",
0xA204 : "10 Mbit ARCnet",
0xA205 : "10 Mbit ARCnet",
0xA206 : "10 Mbit ARCnet",
},
0x157C : { 0x8001 : "PCI Y2K Compliance Card",
},
0x1584 : { 0x5054 : "VAS Vetronix Automotive Service",
4003 : "VAS Vetronix Automotive Service",
},
0x1586 : { 0x0803 : "",
},
0x1588 : { 0x1100 : "PAX.ware 1100 dual Gb classifier engine",
0x2000 : "SNP 8023 packet classifier - AMD component",
0x8023 : "PAX.ware 100 packet classifier",
},
0x158B : { 0x0005 : "Standar HSP Modem",
0x0015 : "Standar HSP Modem Series",
},
0x1592 : { 0x0781 : "Multi-IO Card",
0x0782 : "Parallel Port Card (EPP)",
0x0783 : "Multi-IO Card",
0x0785 : "Multi-IO Card",
0x0786 : "Multi-IO Card",
0x0787 : "Multi-IO Card 2 series",
0x0788 : "Multi-IO Card",
0x078A : "Multi-IO Card",
},
0x15A2 : { 0x0001 : "PCI Bus Analyzer/Exerciser",
},
0x15AD : { 0x0405 : "VMWare Player 3.1.6 Software Driver",
0x0710 : "Virtual SVGA",
0x0720 : "VMware PCI Ethernet Adapter",
0x0740 : "VMWare VMCI Bus Device",
0x0770 : "Standard Enhanced PCI to USB Host Controller",
0x0778 : "Sabrent USB-to-Parallel Adapter",
0x07B0 : "VMware vSphere 4 PCI Ethernet Adapter",
0x0801 : "PCI Memory Controller",
0x1975 : "High Definition Audio Codec",
0x1977 : "High Definition Audio Controller",
},
0x15B0 : { 0x0001 : "Pctel",
0x0003 : "Pctel",
0x2BD0 : "soft56k voice",
},
0x15B3 : { 0x5274 : "InfiniBridge",
0x5A44 : "InfiniHost I",
0x6274 : "InfiniHost III Lx",
0x6278 : "InfiniHost TM III Ex",
0x6282 : "MT25218 [InfiniHost III Ex]",
0x634A : "Mellanox ConnectX VPI (MT2548) - PCIe 2.0 2.5GT/s",
0x6732 : "ConnectX VPI (MT26418) - PCIe 2.0 5GT/s",
},
0x15B8 : { 0x3009 : "Analog output board",
},
0x15BC : { 0x0101 : "DX2+ FC-AL Adapter",
0x0103 : "4 Port Fibre Channel Controller",
0x1200 : "Agilent QX4 Fibre Channel Controller",
0x2530 : "HP Communications Port",
0x2531 : "HP Toptools Remote Control Adapter",
0x2532 : "HP Toptools Remote Control Adapter",
0x2929 : "PCI/PCI-X Bus Analyzer",
},
0x15C2 : { 0x0038 : "part of the iMon-IR-RC-Display-Kit",
},
0x15D1 : { 0x0001 : "TriCore 32-bit Single-chip Microctrlr",
0x0003 : "6 Port Optimized Comm Ctrlr (SPOCC)",
0x0004 : "Infineon Technologies AG",
0x000B : "TPM",
},
0x15D7 : { 0x56 : "hcf 56",
},
0x15D8 : { 0x9001 : "",
},
0x15D9 : { 0x9876 : "4567",
},
0x15DC : { 0x0001 : "PCI Cryptography Module",
},
0x15DD : { 0x7664 : "idt high audio",
0x7680 : "SIGMATEL STAC 92XX C-Major HD Audio",
0x769 : "9200 HD ",
0x7690 : "You'll Love me 4 this/ visit http://wendhelofopportunity.info Support Me!",
0x8384 : "Intel Audio Studio",
0x9876 : "1",
},
0x15E0 : { 0x7134 : "01",
},
0x15E2 : { 0x0500 : "Internet PhoneJack PCI Card",
},
0x15E6 : { 0x0000 : "v.90 Lucent Modem",
},
0x15E7 : { 0x755 : "NTDS Parallel Adapter",
},
0x15E8 : { 0x0130 : "Wireless NIC",
0x0131 : "InstantWave HR PCI card",
},
0x15E9 : { 0x1841 : "ATA controller",
},
0x15EF : { 0x0028 : "SigmaTelHigh Definition Audio CODEC",
0x24c5 : "VIA-Vynil v700b",
0x7616 : "SigmaTelHigh Definition Audio CODEC",
},
0x15F1 : { 0x2F30 : "Conexant HSFi",
},
0x15F2 : { 0x0001 : "Spot RT",
0x0002 : "Spot RT #2",
0x0003 : "Spot Insight",
},
0x160A : { 0x3184 : "Via VT6656 Wireless Lan Adapter",
},
0x1616 : { 0x0409 : "16-Bit",
},
0x1619 : { 0x0400 : "Two Port Intelligent Sync Comms Card",
0x0440 : "Four Port Intelligent Sync Comms Card",
0x0610 : "One Port Intelligent Sync Comms Card",
0x0620 : "Two Port Intelligent Sync Comms Card",
0x0640 : "Four Port Intelligent Sync Comms Card",
0x1610 : "One Port Intelligent Sync Comms Card",
0x1612 : "One Port Intelligent Sync Comms Card",
0x2610 : "G.SHDSL Intelligent Sync Comms Card",
0x3640 : "Four Port Intelligent Sync Comms Card",
0x4620 : "Two Port Intelligent Sync Comms Card",
0x4640 : "Four Port Intelligent Sync Comms Card",
0x5621 : "Two Port Intelligent Sync Comms Card",
0x5641 : "Four Port Intelligent Sync Comms Card",
0x6620 : "Two Port Intelligent Sync Comms Card",
},
0x1621 : { 0x0020 : "4 in/4 out Professional Digital Audio Card",
0x0021 : "2 in/6 out Professional Digital Audio Card",
0x0022 : "6 in/2 out Professional Digital Audio Card",
0x0023 : "2 in/2 out Professional Digital Audio Card",
0x0024 : "16 in/16 out AES/EBU Audio Card",
0x0025 : "16 in/16 out AES/EBU Audio Card w/SRC",
},
0x1629 : { 0x1003 : "Format Synchronizer v3.0",
0x2002 : "Fast Universal Data Output",
},
0x162D : { 0x0100 : "Repeographics controller",
0x0101 : "Reprographics Controller",
0x0102 : "Reprographics Controller",
0x0103 : "Reprographics Controller",
},
0x162F : { 0x1111 : "General Purpose Relay Card",
0x1112 : "Matrix Card",
},
0x1638 : { 0x1100 : " WL11000P",
},
0x163B : { 0x2416 : "DVR Video Capture Card 16CH",
},
0x163C : { 0x3052 : "RS56/HSP-PCI",
0xFF02 : "PCI Bridge - 244E",
},
0x164F : { 0x0001 : "PCI interface chip",
0x0002 : "PCI interaface chip",
},
0x1657 : { 0x0646 : "Brocade 400 series PCIe HBA",
},
0x1658 : { 0x0704 : "DIG 704 PCI - Interface with Millisecond Timer and Interrupts",
},
0x165A : { 0xC100 : "PCI camera link video capture board",
0xD200 : "PCI digital video capture board",
0xD300 : "PCI digital video capture board",
0xF001 : "PCI-E camera link video capture board",
},
0x165C : { 0x0002 : "FT232BL",
},
0x165F : { 0x2000 : "16 Channel Audio Capture Card",
},
0x1668 : { 0x0100 : "PCI to PCI Bridge",
},
0x166D : { 0x0001 : "",
0x0002 : "MIPS BCM1125/BCM1250 processors",
},
0x1676 : { 0x1001 : "Realtek AC' 97 Audio Driver",
},
0x1677 : { 0x20ad : "Profibus DP / K-Feldbus / COM",
},
0x167F : { 0x4634 : "FOB-IO Card",
0x4C32 : "L2B PCI Board",
0x5344 : "FOB-SD Card",
0x5443 : "FOB-TDC Card",
0xF0B2 : "ibaFOB-2io-D",
0xF0B4 : "ibaFOB-4io-D",
},
0x1681 : { 0x0050 : "Hercules WiFi PCI 802.11G",
},
0x1682 : { 0x9875 : "",
},
0x1688 : { 0x0013 : "",
},
0x168C : { 0x001c : "pciven_10ac&dev_ooo",
0x0002 : "Atheros AR5B95 Wireless LAN 802.11 a/b/g/n Controller",
0x0003 : "TP-LINK 450Mbps Wireless N Adapter",
0x0007 : "Wireless Network Adapter",
0x0011 : "11a/b/g Wireless LAN Mini PCI Adapter",
0x0012 : " PCIVEN_1217&DEV_7130&SUBSYS_FF501179&REV_01 DELL Latitude C510 as mini-PCI board behind the larg",
0x0013 : "Netgear RangeMax WPN311 PCI Wireless NIC",
0x0019 : "802.11a Wireless Adapter",
0x001A : "http://support1.toshiba-tro.de/tools/updates/atheros-wlan/atheros-wlan-xp-7702331.zip",
0x001B : "802.11abg NIC",
0x001c : "Wireless Network Adapter",
0x001C : "Atheros AR5BXB63 WWAN Chip",
0x001c : "AR5006EX AR5423a",
0x001D : "PCIVEN_168C&DEV_002E&SUBSYS_E034105B&REV_014&124A40C8&0&00E1",
0x002 : "the drivers for this device are not installed",
0x0023 : "802.11a/b/g/nБеспроводной PC",
0x0024 : "Atheros 802.11a/b/g/n",
0x0027 : "Atheros AR5B95 Wireless LAN 802.11 a/b/g/n Controller",
0x002A : "Atheros AR5B91",
0x002B : "Atheros AR5B195 ",
0x002C : "Wireless 802.11 a/b/g/n Dualband Network Adapter (PCI-Express)",
0x002D : "802.11b/g/n",
0x002E : "Atheros ar9285 PCI Capabilities: Offset ID Description ",
0x0030 : "Killer Wireless - N",
0x0032 : "Atheros AR9485",
0x0034 : "802.11a/b/g/n",
0x0037 : "Atheros AR1111 WB-EG Wireless Network Adapter",
0x003e : "1",
0x007 : "Wireless Network Adapter",
0x0280 : "PCIVEN_168C&DEV_002B&SUBSYS_30AF185F",
0x032 : "Dell Wireless DW1703 802.11b/g/n",
0x1014 : "Atheros AR5212 802.11abg wireless Drivers",
0x14F1 : "PCIVEN_168C&DEV_001A&SUBSYS_04181468&REV_014&FCF0450&0&10A4",
0x168C : "PCIVEN_168C",
0x1a3b : "802.11a/b/g/n Wireless PCI Adapte",
0x3002 : "Bluetooth 3.0",
0x6666 : "Atheros AR5B95 Wireless LAN 802.11 a/b/g/n Controller",
0x9876 : "Atheros AR5B95 Wireless LAN 802.11 a/b/g/n Controller",
0xFF1B : "Wireless LAN G",
0xFF96 : "LAN-Express AS IEEE 802.11g miniPCI adapter",
},
0x1693 : { 0x0212 : "EPONINE ESR-PCI Board",
0x0213 : "EPONINE MTM120 PCI Board",
},
0x16AE : { 0x000A : "Crypto Accelerator",
0x1141 : "Crypto Accelerator",
},
0x16CA : { 0x0001 : "Solid State Disk",
},
0x16EC : { 0x0116 : "RealTek 8169S chip",
0x0303 : "U.S. Robotics 56K FAX USB V1.1.0 / V.92 USB modem",
0x1007 : "U.S. Robotics 56K Win INT",
0x2013 : "U.S. Robotics 56K Voice Host Int",
0x2F00 : "http://www.usr.com/support/product-template.asp?prod=5660a",
0x2f12 : "U.S.Robotic (A- Modem/PCI)",
0x3685 : "Wireless Access Adapter Model 022415",
0x5685 : "U.S. Robotics 56K Voice Host Int (A-Modem/ PCI)",
},
0x170B : { 0x0100 : "Crypto Aceletator",
},
0x1710 : { 0x5812 : "itech numeric small keyboard",
0x9835 : "2 serial",
},
0x1712 : { 0x3038 : "usb",
0x7130 : "unknown",
},
0x1725 : { 0x7174 : "VSC7174 PCI/PCI-X SATA Controller",
},
0x1734 : { 0x007a : "ATI Rage XL (rev 27)",
0x1011 : "Adaptec AIC-7902 Dual Channel U320 SCSI",
0x1012 : "Serverworks Southbridge with RAID/IDE (rev a0)",
0x1013 : "Broadcom Corp. NetXtreme Gigabyte Ethernet",
0x10b9 : "SAS 3000 series",
},
0x1737 : { 0x0071 : "Dual Band Wireless N USB Network Adapter",
0x1032 : "Linksys Instant Gigabit Desktop Network Interface",
},
0x173B : { 0x03E8 : "Gigabit Ethernet Adapter",
0x03EA : "Gigabit Ethernet Adapter",
},
0x1743 : { 0x8139 : "Fast Ethernet Adapter with ROL",
},
0x174B : { 0x0260 : "Saphire Radeon 9250",
0x0261 : "Sapphire Radeon 9250 - Secondary",
0x7176 : "RADEON 9000 ATLANTIS PRO",
0x7177 : "RADEON 9000 ATLANTIS PRO - Secondary",
0x7244 : "Sapphire ATI X1950 XT",
0x7C12 : "RADEON 9200 ATLANTIS - Secondary",
0x7C13 : "RADEON 9200 ATLANTIS",
0x9501 : "ATI Radeon HD 3450",
0xE106 : "Graphics Chipset ATI Radeon HD 4300/4500 Series ",
0xe131 : "ATI 4870",
0xE140 : "Sapphire HD 5870 1GB GDDR5",
},
0x1753 : { 0x1001 : "VP500",
0x1004 : "VP1000",
},
0x1755 : { 0x000 : "",
0x0000 : "Au1500 Processor",
},
0x17A1 : { 0x0128 : "USB2.0 JPEG WebCam ",
},
0x17AA : { 0x7145 : "Mobility ATI Radeon X1400",
},
0x17AF : { 0x4150 : "200",
0x7291 : "RV560",
},
0x17C0 : { 0x12ab : "intel",
},
0x17CC : { 0x1978 : "usb 2.0 device controller",
0x2280 : "USB 2.0 Device Controller",
},
0x17D5 : { 0x5831 : "Xframe 10GbE PCI-X Adapter",
0x5832 : "Xframe II 10GbE PCI-X 2.0 Adapter",
0x5833 : "E3100 PCI-Express 10Gb Ethernet Interface",
},
0x17E9 : { 0x02a7 : "USB VGA/DVI Adapter UV-D4A1-B",
},
0x17EE : { 0x4153 : "RV350",
},
0x17F3 : { 0x1010 : "D1010",
0x1011 : "D1011",
0x1030 : "M1030",
0x2010 : "M2010",
0x3010 : "M3010",
0x6021 : " ",
0x6036 : " ",
0x6040 : "R6040x",
0x6060 : " modem",
0x6061 : " V90479. 1",
},
0x17FE : { 0x2220 : "Generic IEEE 802.11b/g Wireless LAN Card",
},
0x1813 : { 0x3059 : "AC97 Enhanced Audio Controller - the 8251 controller is different",
0x4000 : "intel V.92 HaM Modem",
0x4100 : "Intel HaM V.92 Modem",
},
0x1814 : { 0x0001 : "...B742000",
0x0101 : "2460 802.11b",
0x0201 : "PCIVEN_1814&DEV_3090&SUBSYS_1451033",
0x0201 : "RT 3070",
0x0201 : "001167F044E5",
0x0201 : "RT2560F",
0x0201 : "WMP54G",
0x0301 : "RT2561",
0x0301 : "RT2561",
0x0302 : "RT2525 2.4GHz transceiver + RT2560 MAC/BBP",
0x0401 : "RT 2661",
0x0601 : "RT2860T",
0x0701 : "RT2860T",
0x0781 : "RT2790T/RT2860/RT2890/RT2700E",
0x1418 : "0x14FI",
0x14F1 : "0x1814",
0x201 : "25601814&REV_01",
0x3060 : "RT3060",
0x3090 : "Ralink RT3090",
0x3290 : "RT3290",
0x3298 : "-",
0x3592 : "RT3592",
0x5360 : "RT5360 ",
0x5390 : "RT5390",
0x539B : "RT5390R",
0x9876 : "b8341462",
},
0x186C : { 0x1014 : "Atheros 802.11abg",
},
0x1888 : { 0x0301 : "",
0x0601 : "",
0x0710 : "",
0x0720 : "",
0x2503 : "Video Capture (10 bit High qualtiy cap)",
0x2504 : "Video Capture",
0x3503 : "VGA Geforce4 MX440",
0x3505 : "VGA Geforce4 Ti4200",
},
0x18C9 : { 0x1011 : "Video processor",
0x1012 : "Video processor",
0x1013 : "Video processor",
0x1014 : "Video processor",
0x1015 : "Video processor",
0x1016 : "Video processor",
0x2011 : "Framegrabber",
0x2012 : "Framegrabber",
0x2013 : "Framegrabber",
0x2014 : "Framegrabber",
0x2015 : "Framegrabber",
0x2016 : "Framegrabber",
0x2017 : "Framegrabber",
0x2021 : "Framegrabber",
0x3011 : "Video Output Board",
},
0x18CA : { 0x0020 : "Volari Z series (Select GPU Graphic Drivers",
0x0040 : "Volari Family Z Series",
},
0x18F7 : { 0x0001 : "ESCC-PCI-335",
0x0002 : "422/4-PCI-335",
0x0004 : "422/2-PCI-335",
0x000a : "232/4-PCI-335",
},
0x1904 : { 0x2031 : "controladora ethernet",
0x8139 : "Realtek RTL8139 PCI Fast Ethernet Adapter",
0x8139 : "Realtek RTL8139 PCI Fast Ethernet Adapter",
},
0x1910 : { 0x0001 : "Seaway Network Content Accelerator",
},
0x1912 : { 0x0014 : "usb3.0 renesas",
0x0015 : " nec",
0x0015 : "Renesas Electronics USB 3.0 Host Controller",
},
0x1969 : { 0x1026 : "PCI-E ETHERNET CONTROLLER ",
0x1048 : "Gigabit Ethernet 10/100/1000 Base-T Controller",
0x1060 : "PCI-E Fast Ethernet Controller",
0x1062 : "Atheros AR8132 PCI-E Контроллер Fast Eth",
0x1062 : "Gigabit Ethernet 10/100/1000 Base-T Controller",
0x1063 : "Atheros AR8131 PCI-E Gigabit Ethernet Controller",
0x1073 : "Atheros AR81512 ",
0x1083 : "Atheros AR8151 PCI-E Gigabit Ethernet Controller (NDIS 6.20)",
0x1090 : "Fast Ethernet",
0x1091 : "PCI-E Gigabit Ethernet Controller",
0x168c : "Gigabit Ethernet 10/100/1000 Base-T Controller ",
0x1969 : "Gigabit Ethernet 10/100/1000 Base-T ",
0x2048 : "Fast Ethernet 10/100 Base-T Controller",
0x2049 : "der",
0x2060 : "AR8152 v1.1 Fast Ethernet",
0x2061 : "Ethernet Controller",
0x2062 : "Qualcomm Atheros AR8152/8158",
0x4747 : "VEN_1969",
0x9876 : "Fast Ethernet 10/100 Base-T Controller ",
},
0x1971 : { 0x0001 : "PCIVEN_1971&DEV_0000&SUBSYS_00021028&REV_004&2",
0x1011 : "PCIVEN_1971&DEV_1011&CC_FF00",
0x1021 : "",
},
0x197B : { 0x0250 : "JMC250 PCI Express",
0x0256 : "JMC260 PCI Express Fast Ethernet",
0x0260 : "JMC260 PCI Express Fast Ethernet",
0x1234 : "1234567",
0x197b : "JMB38X SD/MMC Host Controller ",
0x2360 : "JMB36X",
0x2361 : "PCI Express to SATA II and PATA Host Controller",
0x2363 : "JMicron JMB362/JMB363 AHCI Controller",
0x2366 : "JMicron JMB366 AHCI/IDE Controller",
0x2368 : "IDE Comtroller",
0x2380 : "IEEE 1394 Host Controller",
0x2381 : "JMB38X SD Host Controller",
0x2382 : "JMB38X SD/MMC Host Controller ftp://driver.jmicron.com.tw/CardReader/Windows/",
0x2383 : "JMB38X MS Host Controller",
0x2384 : "JMB38X xD Host Controller",
0x2391 : "Intel",
0x2392 : " JMB38X SD/MMC Host Controller",
0x7002 : "JMB38X SD/MMC Host Controller",
},
0x198a : { 0x0210 : "XMC-210",
0x0220 : "XMC-220",
0x0230 : "XMC-230",
0x0240 : "XMC-240",
0x1180 : "PCIe-180",
0x1280 : "PCIe-280",
0x198a : "PCIe-180",
0x402F : " BenNUEY PCIX",
0x4030 : "H100-PCIX",
0x4031 : "BenNUEY PCI-104-V4",
0x4032 : "BenONE-PCIe",
0x4033 : "BenONE-Xilinx-Kit-ROHS",
0x4034 : "BenNUEY PCIX RoHS",
},
0x19a2 : { 0x0710 : "Emulex OneConnect 10Gb NIC (be3) (rev01)",
0x0712 : "Emulex OneConnect 10Gb iSCSI Initiator (be3) (rev 01)",
0x0714 : "Emulex OneConnect 10Gb FCoE Initiator (be3) (rev 02)",
},
0x19AC : { 0x0001 : "Crypto Accelerator",
},
0x19B6 : { 0x110c : "Atheros chipset for 802.11a/b/g",
},
0x19E3 : { 0x5801 : "DDRdrive X1",
0x5808 : "DDRdrive X8",
0xDD52 : "DDRdrive X1-30",
},
0x1B13 : { 0x0001 : "nVidia Corporation NV17",
},
0x1B21 : { 0x1041 : "USB 3.0 Host Controller Driver for Windows 7",
0x1042 : "Asmedia ASM104x USB 3.0 Host Controller",
},
0x1B6F : { 0x7023 : "Etron USB 3.0 Extensible Host Controller",
},
0x1B73 : { 0x1000 : "PCIVEN_1000&DEV_0020&SUBSYS_10301000&REV_01PCIVEN",
0x1100 : "USB 3.0 eXtensibile Host controller",
},
0x1c39 : { 0x0300 : "Pegasus Board PCI-e interface",
},
0x1DE1 : { 0x0045 : "Tekram SAS860 Embedded 8xSAS/SATAII RAID",
0x0058 : "Tekram Elrond 8xSAS/SATAII RAID",
0x0391 : "SCSI ASIC",
0x2020 : "SCSI Controller",
0x690C : "IDE Cache Controller",
0xDC29 : "Bus Master IDE PCI 2 controllers",
},
0x2001 : { 0x3C19 : "USB <=> Wireless N 150 Adapter",
0xF103 : ".",
},
0x2646 : { 0x0001 : "22323",
0x2646 : "22323",
},
0x3388 : { 0x0020 : "Universal PCI-PCI Bridge (transparent mode)",
0x0021 : "ZS095A0",
0x0022 : "PCI-PCI Bridge",
0x0026 : "Universal PCI-PCI Bridge (transparent mode)",
0x0028 : "Dual Mode PCI-X-to-PCI-X Bridge (transparent mode)",
0x0029 : "Dual Mode PCI-X-to-PCI-X Bridge (non-transparent mode)",
0x0030 : "Transparent PCI-X-to-PCI-X Bridge",
0x0031 : "Synchronous 32-Bit",
0x8011 : "CPU to PCI Bridge",
0x8012 : "PCI to ISA Bridge",
0x8013 : "EIDE Controller",
},
0x3D3D : { 0x0001 : "GLint 300SX",
0x0002 : "GLint 500TX",
0x0003 : "GLint",
0x0004 : "3C0SX",
0x0005 : "Permedia",
0x0006 : "GLint MX",
0x0007 : "3D Extreme",
0x0008 : "GLint Gamma G1",
0x0009 : "Permedia2v",
0x000A : "8086",
0x000C : "Permedia 3",
0x000D : "GLINT R4",
0x000E : "GLINT Gamma G2",
0x0020 : "0x0024",
0x0030 : "0x030000",
0x0100 : "Permedia II",
0x1004 : "Permedia",
0x3D04 : "Permedia",
0x3D07 : "same as above? I have no idea",
0xFFFF : "GLint VGA",
},
0x4005 : { 0x0300 : "PCI Audio Device",
0x0308 : "PCI Audio Device + modem",
0x0309 : "PCI Input Controller",
0x1064 : "GUI Accelerator",
0x2064 : "GUI Accelerator",
0x2128 : "GUI Accelerator",
0x2301 : "GUI Accelerator",
0x2302 : "GUI Accelerator",
0x2303 : "GUI Accelerator",
0x2364 : "GUI Accelerator",
0x2464 : "GUI Accelerator",
0x2501 : "GUI Accelerator",
0x4000 : "Audio Chipset",
},
0x4144 : { 0x0040 : "Virtex-E Bridge",
0x0041 : "Virtex-II Bridge",
0x0042 : "Virtex-II Bridge",
0x0043 : "Virtex-II Pro Bridge",
0x0044 : "Virtex-II Pro PCI/PCI-X Bridge",
0x0045 : "Virtex-II Bridge",
0x0046 : "Virtex-II Bridge",
0x0049 : "Virtex-II Pro PCI",
0x004A : "Virtex-II Pro PCI-X Bridge",
0x004F : "Virtex-II Pro PCI-X Bridge",
0x0050 : "Virtex-4LX Bridge",
0x0051 : "ADM-XRC-5T1",
0x0052 : "Xilinx Virtex 5 PMC",
0x0056 : "Virtex 5 AMC FPGA board",
0x0057 : "Xilinx Virtex 5 FPGA PMC ",
0x0058 : "VXS FPGA and PMC Carrier Board",
0x005B : "ADM-XRC-5T2 with JPEG 2000 devices",
0x005C : "FPGA PMC with Analog I/O Interface",
0x005F : "As per XRC-5T2 but with 6 JPEG2000 devices",
0x0300 : "Xilinx Virtex 6 FPGA XMC",
0x0301 : "Xilinx Virtex 6 FPGA XMC",
0x0303 : "Full lenght PCI Express Xilinx Virtex-6 FPGA platform",
0x0305 : "Full length PC Card Xilinx Virtex-6 FPGA platform",
},
0x416C : { 0x0100 : "Puerto paralelo PCI",
0x0200 : "",
},
0x4348 : { 0x1453 : "WCH353L",
0x3253 : "SIE9835 PCI=>DUAL SERIAL",
0x5053 : "5050",
0x7173 : " CH35X",
},
0x4C53 : { 0x0000 : "Diagnostics Device",
0x0001 : "Diagnostics Device",
},
0x4D51 : { 0x0200 : "",
},
0x4E8 : { 0x618d : "epic 4g smartphone (GT B5330)",
},
0x5053 : { 0x2010 : "Daytona Audio Adapter",
},
0x5136 : { 0x4678 : "S S Technologies",
},
0x5143 : { 0x9204 : "WAN Card Lenovo Notebook",
},
0x5333 : { 0x0551 : "86C551",
0x5333 : "S3 86c765",
0x5631 : "86C325",
0x8800 : "86C866",
0x8801 : "86C964",
0x8810 : "86C732-P",
0x8811 : "8622mcq04",
0x8812 : "86CM65?",
0x8813 : "86C764",
0x8814 : "86C767",
0x8815 : "86CM66",
0x883D : "86C988",
0x8870 : "Fire GL",
0x8880 : "86C868",
0x8881 : "86C868",
0x8882 : "86C868",
0x8883 : "86C868",
0x88B0 : "86C928",
0x88B1 : "86C928",
0x88B2 : "86C928",
0x88B3 : "86C928",
0x88C0 : "86C864",
0x88C1 : "86C864",
0x88C2 : "86C864",
0x88C3 : "86C864",
0x88D0 : "86C964",
0x88D1 : "86C964",
0x88D2 : "86C964",
0x88D3 : "86C964",
0x88F0 : "86C968",
0x88F1 : "86C968",
0x88F2 : "86C968",
0x88F3 : "86C968",
0x8900 : "86C775",
0x8901 : "pciven_5333dev_8C2E&SUBSYS_00011179&REV_054&74C6",
0x8902 : "86C551",
0x8903 : "",
0x8904 : "86C365/366",
0x8905 : "86c765",
0x8906 : "86c765",
0x8907 : "86c765",
0x8908 : "9711 MCN74",
0x8909 : "7699688",
0x890A : "0x00091011",
0x890B : "9726 c19394.00",
0x890C : "86C765",
0x890D : "86C765 Trio64V+ compatible",
0x890E : "9711 MCN74",
0x890F : "86c765",
0x8A01 : "86C375/86C385",
0x8A10 : "86C357",
0x8A11 : "86C359",
0x8A12 : "86C359",
0x8A13 : "86C368",
0x8A20 : "86C391",
0x8A21 : "86C390",
0x8A22 : "86c398",
0x8A23 : "86C394-397",
0x8A25 : "86C370",
0x8A26 : "86C395B",
0x8C00 : "85C260",
0x8C01 : "86C260",
0x8C02 : "86C240",
0x8C03 : "86C280",
0x8C10 : "86C270/274/290/294",
0x8C12 : "86C270/274/290/294",
0x8C13 : "82C294",
0x8C22 : "86C508",
0x8C2A : "86C544",
0x8C2B : "86C553",
0x8C2C : "86C564",
0x8C2D : "86C573",
0x8C2E : "86C584",
0x8C2F : "86C594",
0x8D01 : "86C380/381",
0x8D02 : "86c387",
0x8D04 : "86C410",
0x8E00 : "86C777/787",
0x8E01 : "86C732",
0x9102 : "86c410",
0x9876 : "86C390",
0xCA00 : "86C617",
},
0x544C : { 0x0350 : "IAM",
},
0x5555 : { 0x0003 : "Digital Video OEM computer module",
},
0x5853 : { 0x0001 : "n/a",
0x0002 : "n/a",
},
0x6666 : { 0x0001 : "PCCOM4",
0x0002 : "PCCOM8",
},
0x7d1 : { 0x3304 : "802.11N usb wifi device",
0x3c03 : "Same chipset of RALINK RT2500",
0x3C07 : "PCIVEN_1799&DEV_700F&SUBSYS_700F1799&REV_203&61AAA01&0&48",
},
0x8080 : { 0x1040 : "VIA 82C259 rev 0",
},
0x8086 : { 0x27B8 : "Intel(R) 82801GB/GR (ICH7 Family) LPC Interface Controller",
0x0008 : "Extended Express System Support Ctrlr",
0x0011 : "Ethernet Controller",
0x0042 : "Intel Q57/H55 Clarkdale (Onboard on D2912-A1x)",
0x0046 : "Intel Graphics Media Accelerator HD",
0x0054 : "Audio",
0x0082 : "Centrino Advanced-N 6205 ",
0x0083 : "Intel PROSet/Wireless Software and Drivers for Windows 7 32-Bit",
0x0084 : "Intel Wireless Link WiFi 1000",
0x0085 : "Intel Centrino(R) Advanced-N 6205",
0x0087 : "00E1",
0x008A : "Intel Centrino Wireless-N1030",
0x008B : "Intel(R) Centrino(R) Wireless-N 1030 ",
0x0091 : "Intel Centrino Advanced-N 6230",
0x0102 : "Intel HD Graphics 2000",
0x0106 : "2nd Generation Intel Core Processors with Intel HD Graphics 3000/2000",
0x010A : "Lenovo TS130 Intel Video Adapter HD",
0x0111 : "Intel Graphics Conroller",
0x0116 : "Intel HD Graphics 3000",
0x0123 : "hardwareids",
0x0162 : " Core I7",
0x0166 : "3rd Generation Intel HD Graphics 4000",
0x0189 : "Intel Centrino Wireless Bluetooth 3.0 + High Speed Adapter",
0x027A : "Mobile Intel(R) 945 Express Chipset Family",
0x027D : "Mobile PCI-to-PCIsdsdsdI2)",
0x0283 : "Intel(R) ICH8 Family SMBus Controller",
0x0308 : "PCI Audio Device + modem",
0x0309 : "I/O Processor PCI-to-PCI Bridge Unit",
0x030D : "I/O Companion Unit PCI-to-PCI Bridge",
0x0318 : "General Purpose PCI Processor Address Translation Unit",
0x0319 : "General Purpose PCI Processor Address Translation Unit",
0x0326 : "I/OxAPIC Interrupt Controller",
0x0327 : "I/OxAPIC Interrupt Controller B",
0x0329 : "PCI Express-to-PCI Express Bridge A",
0x032A : "PCI Express-to-PCI Express Bridge B",
0x032C : "PCI Express-to-PCI Express Bridge",
0x0330 : "A-Segment Bridge",
0x0331 : "A-Segment IOAPIC",
0x0332 : "B-Segment Bridge",
0x0333 : "B-Segment IOAPIC",
0x0334 : "Address Translation Unit",
0x0335 : "PCI-X Bridge",
0x0336 : "Address Translation Unit (ATU)",
0x0340 : "Serial to Parallel PCI Bridge A",
0x0341 : "Serial to Parallel PCI Bridge B",
0x0370 : "Segment-A PCI Express-to-PCI Express Bridge",
0x0371 : "A-Bus IOAPIC",
0x0372 : "Segment-B PCI Express-to-PCI Express Bridge",
0x0373 : "B-Bus IOAPIC",
0x0374 : "Address Translation Unit",
0x0401 : "P040100",
0x0402 : "intel core i5",
0x0482 : "PCI-EISA Bridge (PCEB)hp dx 7300 microwave tower",
0x0483 : "CPU (i486) Bridge (Saturn)",
0x0484 : "SIO ISA Bridge",
0x0486 : "1261028",
0x04A3 : "Mercury/Neptune Cache/DRAM Controller",
0x0500 : "Processor Bus Controller",
0x0501 : "Memory Controller",
0x0502 : "Scalability Port 0",
0x0503 : "Scalability Port 1 / Glob. Perf. Monitor",
0x0510 : "Hub Interface Port 0 (8-bit compatible)",
0x0511 : "Hub Interface Port 2",
0x0512 : "Hub Interface Port 2",
0x0513 : "Hub Interface Port 3",
0x0514 : "Hub Interface Port 4",
0x0515 : "Server I/O Hub (SIOH)",
0x0516 : "Reliabilty",
0x0530 : "Scalability Port 0",
0x0531 : "Scalability Port 1",
0x0532 : "Scalability Port 2",
0x0533 : "Scalability Port 3",
0x0534 : "Scalability Port 4",
0x0535 : "Scalability Port 5",
0x0536 : "Scalability Port Switch Global Registers",
0x0537 : "Interleave Configuration Registers",
0x0600 : "Storage RAID Controller",
0x0780 : "Intel B75 Express Chipset",
0x0800 : "pci/ven_8086&dev_27da&subsys_30b2103c&rev_023&b1bfb68&0&fb",
0x0885 : "Intel Centrino Wireless-N + WiMAX 6150",
0x0887 : "Intel Centrino Wireless-N 2230",
0x0888 : "Intel Centrino Wireless-N 2230",
0x088E : "Intel Centrino Advanced N 6235",
0x0890 : "Network Controller",
0x0894 : "MRMgRH",
0x0896 : "Intel Centrino Wireless-N 130",
0x08AE : "Intel Centrino Wireless-N 100",
0x0960 : "i960 RP Microprocessor/Bridge",
0x0962 : "i960RM/RN Microprocessor/Bridge",
0x0964 : "i960 RP Microprocessor Bridge",
0x0BE1 : "Intel Graphics Media Accelerator 3600 Series",
0x0C05 : "Intel(R) 6 Series/C200 Series Chipset Family SMBus Controller",
0x1000 : "Gigabit Ethernet Controller",
0x1001 : "10/100/1000 Ethernet Controller (Fiber)",
0x1002 : "Pro 100 LAN+Modem 56 CardBus II",
0x1004 : "Gigabit Ethernet Controller (Copper)",
0x1008 : "Gigabit Ethernet Controller (Copper)",
0x1009 : "Intel",
0x100C : "Gigabit Ethernet Controller (Copper)",
0x100D : "Gigabit Ethernet Controller (LOM)",
0x100E : "Intel Pro 1000/MT",
0x100F : "Gigabit Ethernet Controller (copper)",
0x1010 : "Dual Port Gigabit Ethernet Controller (Copper)",
0x1011 : "Gigabit Ethernet Controller (Fiber)",
0x1012 : "Dual Port Gigabit Ethernet Controller (Fiber)",
0x1013 : "Gigabit Ethernet Controller (Copper)",
0x1014 : "Gigabit Ethernet Controller",
0x1015 : "Gigabit Ethernet Controller (LOM)",
0x1016 : "Gigabit Ethernet Controller (LOM)",
0x1017 : "Gigabit Ethernet Controller (LOM)",
0x1018 : "PRO/1000 MT Mobile connection",
0x1019 : "Gigabit Ethernet Controller (LOM)",
0x101A : "Gigabit Ethernet Controller (LOM)",
0x101d : "Dual Port Gigabit Ethernet Controller",
0x101E : "Gigabit Ethernet Controller (Mobile)",
0x1026 : "Gigabit Ethernet Controller",
0x1027 : "Gigabit Ethernet Controller (Fiber)",
0x1028 : "Gigabit Ethernet Controller",
0x1029 : "Fast Ethernet PCI/CardBus Controller",
0x1030 : "PCI Networking device",
0x1031 : "PRO/100 VE Network Connection",
0x1032 : "PRO/100 VE Network Connection",
0x1033 : "multimedia video controller",
0x1034 : "PRO/100 VM Network Connection",
0x1035 : "Phoneline Network Connection",
0x1036 : "Phoneline Network Connection",
0x1037 : "LAN Controller",
0x1038 : "PRO/100 VM/KM Network Connection",
0x1039 : " 82562",
0x103A : "LAN Controller with 82562ET/EZ (CNR) PHY",
0x103B : "LAN Controller with 82562EM/EX PHY",
0x103C : "LAN Controller with 82562EM/EX (CNR) PHY",
0x103D : "PRO/100 VE Network Connection",
0x103E : "PRO/100 VM Network Connection",
0x1040 : "V.92 PCI (DSP) Data Fax Modema",
0x1042 : "PRO/Wireless 2011 LAN PCI Card",
0x1043 : "Intel(R) PRO/Wireless 2100 LAN Card Driver",
0x1048 : "10 Gigabit Ethernet Controller",
0x1049 : "Gigabit Network Connection Interface Controller",
0x104A : "gigabit ethernet",
0x104B : "Gigabit Ethernet",
0x104D : "Intel Gigabit 82566MC",
0x1050 : "PRO/100 VE Network Connection",
0x1051 : "PRO/100 VE Network Connection",
0x1052 : "PRO/100 VM Network Connection",
0x1053 : "PRO/100 VM Network Connection",
0x1054 : "PRO/100 VE Network Connection (mobile)",
0x1055 : "PRO/100 VM Network Connection (mobile)",
0x1059 : "Fast Ethernet PCI/CardBus Controller",
0x105E : "HP NC360T PCIe DP Gigabit Server Adapter",
0x1064 : "82562EZ PLC",
0x1065 : "LAN Controller Intel Corporation 82562ET/EZ/GT/GZ - PRO/100 VE Ethernet Controller",
0x1068 : "1068h 82562ET/EZ/GT/GZ PRO/100 VE Ethernet Controller",
0x1075 : "Gigabit Ethernet Controller",
0x1076 : "Gigabit Ethernet Controller",
0x1077 : "Gigabit Ethernet Controller (Mobile)",
0x1078 : "Gigabit Ethernet Controller",
0x1079 : "Dual Port Gigabit Ethernet Controller",
0x107A : "Dual Port Gigabit Ethernet Controller (Fiber)",
0x107B : "Dual Port Gigabit Ethernet Controller (Copper)",
0x107C : "Gigabit Ethernet Controller (Copper) rev 5",
0x1080 : "FA82537EP - Intel 537EP V.92 (PCI) modem",
0x108B : "Intel network controller (PCIE Gigabit Ethernet)",
0x108c : "Intel Corporation 82573E Gigabit Ethernet Controller (Copper)",
0x108E : "Intel(R) Active Management Technology - KCS",
0x108F : "Intel(R) Active Management Technology - SOL",
0x1092 : "PRO/100 VE Network Controller",
0x1094 : "get PRO2KXP.exe from Intel",
0x1096 : "Intel PRO/1000 EB",
0x109A : "Intel PRO/1000 PL Network Adaptor",
0x109c : "HP E1Q Express",
0x10a7 : "82575EB Gigabit Network Connection",
0x10a9 : "82575EB Gigabit Backplane Connection",
0x10b5 : "Quad Port Gigabit Ethernet Controller",
0x10b9 : "Intel PRO/1000 PT Desktop",
0x10BD : "Intel 82566DM Gigabit Ethernet Adapter",
0x10C0 : "Intel(R) 82562V-2 10/100 Network Connection",
0x10c4 : "Intel 82562GT 10/100 Network Controller",
0x10c4 : "Intel 82562GT 10/100 Network Controller",
0x10c9 : "82576 Gigabit ET Dual Port Server Adapter",
0x10CE : "Intel 82567V-2 Gigabit Network Connection",
0x10d3 : "Intel 82574L Gigabit Ethernet Controller",
0x10d6 : "82566 DM-2-gigabyte",
0x10DE : "Intel Gigabit network connection",
0x10e6 : "82576 Gigabit Network Connection",
0x10e7 : "82576 Gigabit Network Connection",
0x10E8 : "E64750-xxx Intel Gigabit ET Quad Port Server Adapter",
0x10EA : "Intel 82577LM Gigabit LAN Driver ",
0x10EC : "Realtek 171 High Definition Audio",
0x10EF : "Intel 82578DM Gigabit Ethernet Controller",
0x10F0 : "Intel(R) 82578DC Gigabit NIC",
0x10F5 : "Intel 82567LM-2 Gigabit Network Connection",
0x10fb : "10 Gb Ethernet controller",
0x1100 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x1101 : "AGP Bridge",
0x1102 : "Internal Graphics Device",
0x1110 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x1112 : "Internal Graphics Device",
0x1120 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x1121 : "AGP Bridge",
0x1130 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x1131 : "AGP Bridge",
0x1132 : "Internal Graphics Device [810/815 chipset AGP]",
0x1161 : "I/O APIC Device",
0x1162 : "XScale 80200 Companion Chip (FPGA)",
0x1179 : "Dual Port Gigabit Ethernet Controller",
0x12 : "00",
0x1200 : "Network Processor",
0x1209 : "Fast Ethernet Controller for xp pc",
0x1221 : "PCMCIA Bridge",
0x1222 : "IDE Ctrlr",
0x1223 : "Audio Controller",
0x1225 : "Orion Extended Express CPU to PCI Bridge",
0x1226 : "EtherExpress PRO/10",
0x1227 : "LAN Controller with 82562EM",
0x1228 : "Intelligent 10/100 Fast Ethernet Adapter",
0x1229 : "Intel(R) PRO/100 M 00000Desktop Adapter http://downloadmirror.intel.com/8659/eng/LAN_ALLOS_11.2_PV",
0x122D : "System Controller (TSC)",
0x122E : "PCI to ISA Bridge (Triton)",
0x1230 : "IDE Interface (Triton)",
0x1231 : "DSVD Modem",
0x1234 : "PCI to ISA Bridge",
0x1235 : "Mobile System Controller (MTSC)",
0x1237 : "PCI & Memory",
0x1239 : "IDE Interface (Triton)",
0x123B : "PCI to PCI Docking Bridge",
0x123C : "Mobile PCI-to-ISA Bridge (MISA)",
0x123D : "Programmable Interrupt Device",
0x123E : "Integrated Hot-Plug Controller (IHPC)",
0x123F : "Integrated Hot-Plug Controller (IHPC)",
0x1240 : "AGP Graphics Accelerator",
0x124B : "Mobile PCI-to-PCIsdsdsdI2)",
0x124B : "Mobile PCI-to-PCIsdsdsdI2)",
0x124C : "Mobile PCI-to-PCI Bridge (MPCI2)",
0x1250 : "System Controller (TXC)",
0x12D8 : "SIGMATEL STAC 92XX C-Major HD Audio",
0x1360 : "Hub Interface to PCI Bridge",
0x1361 : "Advanced Interrupt Controller",
0x13ca : "VVVVVV",
0x1460 : "Hub Interface-to-PCI Bridge",
0x1461 : "I/OxAPIC Interrupt Controller",
0x1462 : "Hot Plug Controller",
0x1502 : "Intel 82579LM Gigabit Network Card",
0x1503 : "Gigabit Network Connection",
0x150a : "82576NS Gigabit Ethernet Controller",
0x150C : "Intel 82583V Gigabit Ethernet Controller",
0x150d : "82576 Gigabit Backplane Connection",
0x150e : "82580 Gigabit Network Connection",
0x150f : "82580 Gigabit Fiber Network Connection",
0x1510 : "82580 Gigabit Backplane Connection",
0x1511 : "82580 Gigabit SFP Connection",
0x1516 : "82580 Gigabit Network Connection",
0x1518 : "82576NS SerDes Gigabit Network Connection",
0x1521 : "i350 Gigabit Network Connection",
0x1525 : "Intel 82567V-4 Gigabit Network Connection",
0x1526 : "Intel Gigabit ET2 Quad Port Server Adapter",
0x1533 : "Intel I210 Gigabit Network Connection",
0x167D : "PCI Simple Communications Controller",
0x1960 : "i960RP Microprocessor",
0x1962 : "Promise SuperTrak SX6000 IDE RAID Controller",
0x1A12 : "Eicon DIVA Server Voice PRI 2.0 (PCI)",
0x1A13 : "Eicon DIVA Server Voice PRI 2.0 (PCI)",
0x1A20 : "",
0x1A21 : "Host-Hub Interface A Bridge / DRAM Ctrlr",
0x1A22 : "Host to I/O Hub Bridge (Quad PCI)",
0x1A23 : "AGP Bridge",
0x1A24 : "Hub Interface B Bridge",
0x1A30 : "Host-Hub Interface Bridge",
0x1A31 : "AGP Bridge",
0x1A38 : "5000 Series Chipset DMA Engine",
0x1c02 : "sata ahci contoller",
0x1c02 : "Intel(R) Desktop/Workstation/Server Express Chipset SATA AHCI Controller",
0x1C03 : "Intel(R) CPT Chipset Family 6 Port SATA AHCI Controller ",
0x1C22 : "Intel(R) 6 Series/C200 Series Chipset Family SMBus Controller",
0x1C26 : "USB Enhanced Host Controller",
0x1c34 : "pci simple communications controller",
0x1c3a : "Intel Management Engine Interface",
0x1C3b : "Series Chipset Family HECI Controller #2",
0x1C3D : "Intel(R) Active Management Technology - SOL",
0x1C49 : "04",
0x1D3A : "X79/C600 series chipset Management Engine Interface",
0x1e00 : "2 ports IDE Controller",
0x1e08 : "2 ports IDE Controller",
0x1E12 : "rev",
0x1E22 : "SM-Bus Controller of the Intel Z77 Chipset",
0x1e31 : "Intel USB 3.0",
0x1E3A : "Intel Management Engine Interface (MEI)",
0x1E3A : "Intel 7 Series/C216",
0x1E3A : "C216 Chipset - Platform controller hub",
0x1E3D : "Intel(R) AMT LMS_SOL for AMT 8.xx",
0x1E59 : "140889",
0x2000 : "505943621",
0x2014 : "Framegrabber",
0x2048 : "Fast Ethernet 10/100 Base-T Controller",
0x2124 : "PRO/100 VE Network Connection",
0x2125 : "AC97 Audio Controller. website to download - http://www.intel.com/design/chipsets/manuals/29802801.p",
0x2222 : "Intel Management Interface",
0x2255 : "023",
0x2406 : "AC97 Modem Controller / PCI Modem",
0x2410 : "LPC Interface",
0x2411 : "IDE Controller (UltraATA/66)",
0x2412 : "USB Controller",
0x2413 : "SMBus Controller",
0x2415 : "Aureal (AD1881 SOUNDMAX) Placa Me Asaki P3-141",
0x2416 : "AC'97 Modem Controller",
0x2418 : "Hub Interface-to-PCI Bridge",
0x2420 : "LPC Interface",
0x2421 : "IDE Controller (UltraATA/33)",
0x2422 : "USB Controller",
0x2423 : "SMBus Controller",
0x2425 : "Audio controler",
0x2426 : "AC97 Modem Controller",
0x2428 : "Hub Interface-to-PCI Bridge",
0x2431 : "pci bus",
0x2440 : "LPC Interface Bridge",
0x2441 : "IDE Controller (UltraATA/66)",
0x2442 : "USB Controller",
0x2443 : "SMBus Controller",
0x2444 : "USB Controller",
0x2445 : "AC97 Audio Controller",
0x2446 : "AC97 Modem Controller",
0x2448 : "Hub Interface to PCI Bridge",
0x2449 : "82559ER Integrated 10Base-T/100Base-TX Ethernet Controller",
0x244A : "IDE Controller",
0x244B : "IDE Controller",
0x244C : "LPC Interface Bridge",
0x244E : "Hub Interface to PCI Bridge",
0x2450 : "LPC Interface Bridge",
0x2452 : "USB Controller",
0x2453 : "SMBus Controller",
0x2459 : "LAN0 Controller",
0x245B : "IDE Controller",
0x245D : "Multimedia Audio Controller",
0x245E : "Hub Interface to PCI Bridge",
0x2480 : "LPC Interface Bridge",
0x2481 : "IDE Controller (UltraATA/66)",
0x2482 : "USB Controller",
0x2483 : "SMBus Controller",
0x2484 : "USB Controller",
0x2485 : "AC97 Audio Controller",
0x2486 : "AC 97 Modem Controller",
0x2487 : "USB Controller",
0x248A : "UltraATA IDE Controller",
0x248B : "UltraATA/100 IDE Controller",
0x248C : "LPC Interface or ISA bridge: see Notes",
0x248D : "USB 2.0 EHCI Contoroller",
0x24C0 : "LPC Interface Bridge",
0x24C2 : "USB UHCI Controller #1",
0x24C3 : "modem",
0x24C4 : "USB UHCI Controller",
0x24C5 : "Realtek AC97",
0x24C5 : "PCI Simple Communications Controller",
0x24C5 : "VIA Vynil v700b",
0x24c5 : "Soundmax Integrated Digital Audio",
0x24C5 : "Intel 82801 DB DBM/DA AC 97 Audio Controller",
0x24c5 : "Audio Controller",
0x24C6 : "AC97 Modem Controller / PCI Modem",
0x24C7 : "USB UHCI Controller #3",
0x24CA : "IDE Controller (UltraATA/100)",
0x24CB : "IDE Controller (UltraATA/100)",
0x24CC : "LPC Interface Bridge",
0x24CD : "USB EHCI Controller",
0x24D0 : "LPC Interface Bridge",
0x24D1 : "SATA Controller",
0x24D2 : "USB UHCI Controller 1",
0x24D3 : "SMBus Controller",
0x24D4 : "USB UHCI Controller #2",
0x24D5 : "Realtek AC'97 Sound System Software",
0x24D6 : "Motorola SM56 Data Fax Modem",
0x24D7 : "USB UHCI Controller #3",
0x24DB : "EIDE Controller",
0x24DC : "LPC Interface Controller",
0x24DD : "USB EHCI Controller",
0x24DE : "USB UHCI Controller #4",
0x24DF : "SATA Controller (RAID)",
0x2500 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x2501 : "Host Bridge (MCH)",
0x2502 : "",
0x2503 : "",
0x2504 : "",
0x250B : "Host Bridge (MCH)",
0x250F : "AGP Bridge",
0x2520 : "Memory Translator Hub (MTH)",
0x2521 : "Audio Device on High Definition Audio Bus",
0x2530 : "Host-Hub Interface Bridge(A2 step)",
0x2531 : "Host-Hub Interface_A Bridge (DP mode)",
0x2532 : "AGP Bridge",
0x2533 : "Hub Interface_B Bridge",
0x2534 : "Hub Interface_C Bridge",
0x2535 : "PCI Bridge",
0x2536 : "PCI Bridge",
0x2539 : "(Quad Processor mode)",
0x2540 : "Host-HI Bridge & DRAM Controller",
0x2541 : "DRAM Controller Error Reporting",
0x2543 : "HI_B Virtual PCI-to-PCI Bridge",
0x2544 : "HI_B PCI-to-PCI Bridge Error Reporting",
0x2545 : "HI_C Virtual PCI-to-PCI Bridge",
0x2546 : "HI_C PCI-to-PCI Bridge Error Reporting",
0x2547 : "HI_D Virtual PCI-to-PCI Bridge",
0x2548 : "HI_D PCI-to-PCI Bridge Error Reporting",
0x254C : "Host Controller",
0x2550 : "Host Controller",
0x2551 : "Host RAS Controller",
0x2552 : "PCI-to-AGP Bridge",
0x2553 : "Hub Interface_B PCI-to-PCI Bridge",
0x2554 : "Hub I/F_B PCI-to-PCI Bridge Error Report",
0x255d : "Host Controller",
0x2560 : "DRAM Controller / Host-Hub I/F Bridge",
0x2561 : "Host-to-AGP Bridge",
0x2562 : "Integrated Graphics Device",
0x2562 : "SATA RAID CONTROLLER",
0x2570 : " 82848P",
0x2571 : " 82848P",
0x2572 : "Integrated Graphics Device",
0x2573 : " 82848P",
0x2576 : " 82848P",
0x2578 : "DRAM Controller / Host-Hub Interface",
0x2579 : "PCI-to-AGP Bridge",
0x257A : "",
0x257B : "PCI to CSA Bridge",
0x257E : "Overflow Configuration",
0x2580 : "Host Bridge / DRAM Controller",
0x2581 : " 925X/XE?",
0x2582 : "82915g/gv/910gl Express Chipset Family",
0x2582 : "82915g/gv/910gl Express Chipset Family",
0x2584 : "Host Bridge / DRAM Controller",
0x2585 : "",
0x2588 : "Host Bridge/DRAM Controller",
0x2589 : "PCI Express Bridge",
0x258A : "Internal Graphics",
0x2590 : "Mobile Intel(R) 915GM/PM/GMS/910GML Express Processor to DRAM Controller",
0x2592 : "Graphic controller family",
0x25A1 : "LPC Interface Bridge",
0x25A2 : "PATA100 IDE Controller",
0x25A3 : "SATA Controller(IDE Mode)",
0x25A4 : "SMBus Controller",
0x25A6 : "AC'97 Audio Controller",
0x25A7 : "AC'97 Modem Controller",
0x25A9 : "USB 1.1 UHCI Controller #1",
0x25AA : "USB 1.1 UHCI Controller #2",
0x25AB : "Watchdog Timer",
0x25AC : "APIC1",
0x25AD : "USB 2.0 EHCI Controller",
0x25AE : "Hub Interface to PCI-X Bridge",
0x25B0 : "Serial ATA Controller (RAID mode)",
0x2600 : "Hub Interface 1.5",
0x2601 : "PCI Express Port D",
0x2602 : "PCI Express Port C0",
0x2603 : "PCI Express Port C1",
0x2604 : "PCI Express Port B0",
0x2605 : "PCI Express Port B1",
0x2606 : "PCI Express Port A0",
0x2607 : "PCI Express Port A1",
0x2640 : "LPC Interface Bridge",
0x2641 : "LPC Interface Bridge (ICH6-M)",
0x2651 : "SATA Controller",
0x2652 : "SATA RAID Controller",
0x2652 : "SATA Controller",
0x2652 : "SATA Raid Controller",
0x2652 : "AHCI Controller",
0x2653 : "SATA AHCI Controller",
0x2653 : "SATA IDE Controller",
0x2653 : "AHCI Controller",
0x2658 : "USB UHCI Controller #1",
0x2659 : "USB UHCI Controller #2",
0x265A : "USB UHCI Controller #3",
0x265B : "USB UHCI Controller #4",
0x265C : "USB 2.0 EHCI Controller",
0x266 : "VIA AC97 codec incorporated into VT82C686VT8251 SouthbridA/B",
0x2660 : "PCI Express Port 1",
0x2662 : "PCI Express Port 2",
0x2664 : "PCI Express Port 3",
0x2666 : "PCI Express Port 4",
0x2668 : "82801FB (ICH6) High Definition Audio Controller",
0x2669 : "jkn ",
0x266A : "SMBus Controller",
0x266C : "LAN Controller",
0x266D : "http://www.dell.com/support/drivers/us/en/19/DriverDetails/DriverFileFormats?DriverId=R104087&FileId",
0x266E : "VIA AC97",
0x266F : "PATA100 Controller - 266F",
0x2670 : "LPC Interface Controller",
0x2678 : "8280 (ICH6) High Defininition Audio Controller",
0x2680 : "SATA Controller(IDE Mode)",
0x2681 : "631xESB/632xESB SATA AHCI Controller",
0x2682 : "Intel(R) ESB2 SATA RAID Controller",
0x269B : "SMBus Controller",
0x269E : "PATA100 IDE Controller",
0x27 : "ICH7 Family",
0x2770 : "Host Bridge/DRAM Controller",
0x2771 : "Host to PCI Express Bridge",
0x2772 : "Chipset Intel 82945G Express ",
0x2776 : "INTEL(R) 82945G EXPRESS FAMILY",
0x277C : "Intel 975X Express Chipset",
0x2780 : "Graphics device",
0x2782 : "Graphics device: 82915G/GV/910GL Express Chipset Family",
0x2792 : "Mobile Intel(R) 915GM/GMS/",
0x2794 : "Mobile chipset",
0x27A0 : "i945GM Express Chipset",
0x27A1 : "Intel Corporation Mobile 945PM Express PCI Express Root Port",
0x27A2 : "Mobile Intel(R) 945 Express Chipset Family",
0x27A6 : "Intel 945GM/950",
0x27B8 : "PCIVEN_8086&_27B8&SUBSYS_8179DEV1043&REV_013&11583659&0&F8",
0x27BC : "NM10 Family LPC Interface Controller",
0x27c0 : "82801 GB Serial ATA Storage Controllers",
0x27C1 : "AHCI Controller",
0x27c3 : "Raid Controller",
0x27c4 : "SATA IDE Controller",
0x27C5 : "AHCI Controller",
0x27C6 : "Raid Controller",
0x27c8 : "USB UHCI Controller",
0x27c9 : "USB UHCI Controller",
0x27CA : "USB UHCI Controller",
0x27CB : "USB UHCI Controller",
0x27CC : "Intel(R) 82801G (ICH7 Family) USB2 Enhanced Host Controller",
0x27D0 : "Intel(R) 82801G (ICH7 Family) PCI Express Root Port",
0x27D2 : "Intel(R) 82801G (ICH7 Family) PCI Express Root Port",
0x27d8 : "Realtek High Definition Audio Driver FF311179 thequetta.com",
0x27d8 : "Microsoft UAA Bus HD Audio",
0x27D9 : "IDT High Definition Audio Driver ",
0x27DA : "Intel[R] 82801G (ICH7 Family) C- 27DA",
0x27DC : "Intel PRO/100 VE Desktop Adapter",
0x27DC : "Intel PRO/100 VE Desktop Adapter",
0x27DE : "AUDIO (ALC850) << Realtek ",
0x27df : "PATA100",
0x27 : "no",
0x2802 : "INTEL(R) HIGH DEFINITION AUDIO HDMI",
0x2803 : "Intel(R) High Definition Audio HDMI Service",
0x2804 : "IntcDAudModel",
0x2815 : "Intel(R) ICH8M LPC Interface Controller - 2815 Driver",
0x2820 : "SATA IDE Controller:4 port",
0x2821 : "AHCI Controller",
0x2822 : "Raid Controller",
0x2824 : "ICH8 AHCI Controller",
0x2825 : "Intel Q35",
0x2828 : "SATA IDE Controller",
0x2829 : "AHCI Controller",
0x282A : "Raid Controller",
0x283A : "ICH8 Enhanced USB2 Enhanced Host Controller",
0x283E : "SM Bus Controller",
0x284 : "Microsoft UAA bus for HD audio",
0x284B : "Microsoft UAA bus for HD audio",
0x2850 : "PATA Controller",
0x2880 : "Intel Display Audio",
0x2888 : "Q945",
0x2914 : "LPC bridge of ICH9",
0x2916 : "PCI Simple Communications-Controller ",
0x2920 : "SATA IDE Controller:4 port",
0x2921 : "SATA IDE Controller:2 port1",
0x2922 : "AHCI Controller",
0x2923 : "ICH9 AHCI Controller",
0x2925 : "Raid Controller",
0x2926 : "SATA IDE Controller:2 port2",
0x2928 : "SATA IDE Controller:2port1",
0x2929 : "ICH9M/ME AHCI Controller",
0x292D : "SATA IDE Controller:2port2",
0x292E : "SATA IDE Controller:1port2",
0x2930 : "2930",
0x2930 : "Intel ICH9 Family SMBus Controller",
0x2936 : "Intel(R) ICH9 Family USB Univeral Host Controller",
0x293E : "82801IB/IR/IH (ICH9 Family) HD Audio Controller",
0x293E : "82801IB/IR/IH (ICH9 Family) HD Audio Controller",
0x294C : "Intel(R) 82566DC-2 Gigabit Network Connection",
0x2972 : "Onboard Video Device for 82946GZ chips",
0x2986 : "Intel",
0x2987 : "Intel PCI Serial Port",
0x2992 : "Intel(R) Express Chipset video",
0x2993 : "Intel(R) Express Chipset (Dell Version)",
0x2994 : "intel management engine interface",
0x2996 : "IDE Controller",
0x2997 : "Intel Active Management Technology (AMT) - SOL",
0x29a0 : "Intel P965/G965 Processor to I/O Controller",
0x29a1 : " 82G965",
0x29A2 : "Intel 82G965 Graphics and Memory Controller Hub (GMCH)",
0x29A4 : "MRMgRH <a href=",
0x29A6 : "IDE Controller",
0x29B2 : "Intel(R) Q35 Express Chipset Family",
0x29B3 : "Intel",
0x29B4 : "Intel(R) Management Engine Interface (HECI)",
0x29B4 : "",
0x29B6 : "IDE Controller",
0x29B7 : "Serial Over LAN",
0x29C2 : "Intel(R) G33 chipset GMA3100 video Driver",
0x29C2 : "Intel(R) G33 chipset GMA3100 video Driver",
0x29C4 : "Intel ME: Management Engine Interface",
0x29C6 : "IDE Controller",
0x29D4 : "Intel Management Interface",
0x29D6 : "IDE Controller",
0x29E6 : "IDE Controller",
0x29F6 : "IDE Controller",
0x2A02 : "Intel GM965",
0x2A03 : "Intel GM",
0x2A04 : "Intel PCI communication controller-Intel Management Engine Interface update",
0x2A06 : "IDE Controller",
0x2A07 : "Intel PCI Serial Port",
0x2A08 : "Intel(R) Extended Thermal Model MCH",
0x2A12 : "Mobile Intel(R) 965 Express Chipset Family",
0x2A16 : "IDE Controller",
0x2A42 : "Intel Mobile Graphic",
0x2A43 : "Intel Mobile Graphic",
0x2A44 : "IC658",
0x2A46 : "IDE Controller",
0x2a47 : "Active Management Technology - SOL",
0x2A52 : "IDE Controller",
0x2E06 : "IDE Controller",
0x2E12 : "Intel Q45/Q43 Express Chipset",
0x2e13 : "Intel(R) 4 Series Internal Chipset",
0x2E14 : "Intel Management Engine Interface (HECI)",
0x2E15 : "Intel AMT LMS_SOL for AMT 5.xx",
0x2E16 : "IDE Controller",
0x2E17 : "Intel AMT LMS_SOL for AMT 5.xx",
0x2E24 : "Intel Management Engine Interface",
0x2E24 : "Intel Management Engine Interface",
0x2E26 : "IDE Controller",
0x2e29 : "Intel(R) 4 Series Chipset PCI Express Root Port - 2E29",
0x2E32 : "Intel G41 express graphics",
0x2E33 : "ghaphics chipset g41TY",
0x2E33 : "ghaphics chipset g41 ghaphics chipset g41 ",
0x2E46 : "IDE Controller",
0x2E96 : "IDE Controller",
0x2f00 : "multimedia audio device (codec AC97) SoundMAX or VIA",
0x3092 : "I2O 1.5 RAID Controller",
0x3200 : "PCI-X to Serial ATA Controller",
0x3252 : "SUBSYS",
0x3340 : "Host-Hub Interface Bridge",
0x3341 : "AGP Bridge",
0x3342 : "Power Management",
0x3408 : "Intel 7500 Chipset PCIe Root Port",
0x3409 : "Intel 7500 Chipset PCIe Root Port",
0x340A : "Intel 7500 Chipset PCIe Root Port",
0x340B : "Intel 7500 Chipset PCIe Root Port",
0x340C : "Intel 7500 Chipset PCIe Root Port",
0x340E : "Intel 7500 Chipset PCIe Root Port",
0x3410 : "Intel 7500 Chipset PCIe Root Port",
0x3423 : "SRCU21/SRCU31 Microsoft Windows* 2000 Memory Management Files",
0x3464 : "NTPNP_PCI0002",
0x348D : "Gigabit Ethernet Controller",
0x34c5 : "Realtek AC97 (NOT an intel)",
0x3575 : "Host-Hub I/F Bridge / SDRAM Controller",
0x3576 : "Host-AGP Bridge",
0x3577 : "Integrated Graphics Device",
0x3578 : "CPU to I/O Bridge",
0x3579 : "SDRAM Controller / Host-hub Interface",
0x357B : "Integrated Graphics Device",
0x3580 : "Host-Hub Interface Bridge",
0x3581 : "Virtual PCI to AGP Bridge",
0x3582 : "Integrated Graphics Device",
0x3584 : "System Memory Controller",
0x3585 : "Configuration Process",
0x3590 : "Memory Controller Hub",
0x3591 : "Memory Controller Hub",
0x3592 : "Memory Controller Hub",
0x3593 : "MCH Error Reporting Registers",
0x3594 : "DMA Controller Registers",
0x3595 : "PCI Express Port A",
0x3596 : "PCI Express Port B",
0x3597 : "PCI Express Port B",
0x3598 : "PCI Express Port B1",
0x3599 : "PCI Express Port C",
0x359A : "PCI Express Port C1",
0x359B : "Extended Configuration Registers",
0x359E : "MCH Control Registers",
0x360B : "intel simple communication controller",
0x3A00 : "ICH10 4 port SATA IDE Controller",
0x3A02 : "ICH10D SATA Controller",
0x3A03 : "ICH10 AHCI",
0x3A05 : "ICH10D SATA Controller",
0x3A06 : "SATA2(2Port1)",
0x3A14 : "82801JDO ICH10DO",
0x3A1A : "82801JD ICH10D",
0x3A20 : " SATA2(4Port2)",
0x3A22 : "AHCI Controller",
0x3A23 : "ICH10 AHCI",
0x3A26 : "SATA2(2Port2)",
0x3A30 : "INTEL(R) ICH10 Family SMB controller ",
0x3A3E : "Microsoft UAA Bus Driver for High Definition Audio",
0x3a60 : "SM-Bus Controller",
0x3B00 : "LPC Interface Controller",
0x3B01 : "LPC Interface Controller",
0x3B02 : "LPC Interface Controller",
0x3B03 : "LPC Interface Controller",
0x3B06 : "LPC Interface Controller",
0x3B07 : "LPC Interface Controller",
0x3B08 : "LPC Interface Controller",
0x3B09 : "LPC Interface Controller",
0x3B0A : "LPC Interface Controller",
0x3B0B : "LPC Interface Controller",
0x3B0D : "LPC Interface Controller",
0x3B0F : "LPC Interface Controller",
0x3B12 : "LPC Interface Controller",
0x3B14 : "LPC Interface Controller",
0x3B16 : "LPC Interface Controller",
0x3B20 : "SATA IDE 4-Port Desktop",
0x3B21 : "SATA IDE 2-Port Desktop",
0x3B22 : "SATA AHCI 6-Port Desktop",
0x3B23 : "SATA AHCI 4-Port Desktop",
0x3B24 : "SATA Enhanced RAID",
0x3B25 : "SATA Raid Controller",
0x3B26 : "SATA IDE 2-Port Secondary Desktop",
0x3B28 : "SATA IDE 4-Port Mobile",
0x3B29 : "SATA AHCI 4-Port Mobile",
0x3B2B : "SATA Enhanced RAID",
0x3B2C : "SATA Raid Controller",
0x3B2D : "SATA IDE Controller:2 port",
0x3B2E : "SATA IDE 4-Port Mobile",
0x3B2F : "SATA AHCI 6-Port Mobile",
0x3B30 : "SMBus Контроллер",
0x3B32 : "LPC Interface Controller",
0x3b63 : "06",
0x3B64 : "Management Engine Driver",
0x3B64 : "Management Engine Driver",
0x3B64 : "Intel Management Engine Interface",
0x3B64 : "Intel Management Engine Interface",
0x3B64 : "intel",
0x3b65 : "06",
0x3B67 : "Intel(R) Active Management Technology - Serial Over LAN (SOL) ",
0x4000 : "V.90 HaM Modem",
0x402f : "Intel (R) 5400 Chipset QuickData Technology device - 402F",
0x4220 : "Intel 54 MBit/s Notebook WLAN Card",
0x4222 : "Intel 3945ABG Wireless LAN controller",
0x4223 : "Intel (R) PRO/Wireless 2200BG Network Connection",
0x4223 : "Intel (R) PRO/Wireless 2200BG Network Connection",
0x4224 : "802.11a/b/g WLan adapter",
0x4227 : "Intel(R) PRO/Wireless 3945ABG",
0x4229 : "Intel Wireless WiFi Link 4965AGN(supporting 802.11a/b/g/Draft-N)",
0x422B : "Intel(R) Centrino(R) Ultimate-N 6300 AGN",
0x422C : "Broadcom Wifi",
0x422D : "Intel Wireless WiFi Link 4965AGN",
0x4230 : "Intel Wireless WiFi Link 4965AGN",
0x4232 : "Carte Intel WiFi Link 5100 AGN",
0x4233 : "Intel Wireless WiFi Link 4965AGN",
0x4235 : "Intel WiFi Link 5300 AGN",
0x4236 : "Intel(R) WiFi Link 5300 AGN",
0x4237 : "Intel (R) WiFi Link 5100 AGN",
0x4238 : "Intel Centrino Ultimate-N 6300 AGN",
0x4239 : "Intel(R) Centrino(R) Advanced-N 6200 AGN",
0x423A : "PRO/Wireless 5350 AGN [Echo Peak]",
0x423C : "WiMAX/WiFi Link 5150",
0x4318 : "Dell Wireless 1370 WLAN Mini-PCI Card",
0x444E : "Intel TurboMemory",
0x4813 : "Dell Wireless 1370 WLAN Mini-PCI Card",
0x4836 : "2425678",
0x4888 : "intel 3945abg wireless lan controller",
0x5001 : "Modem - PPP",
0x5005 : "Modem - PPPoA",
0x5029 : "AHCI Controller",
0x502A : "SATA Controller",
0x502B : "SATA Controller",
0x5200 : "PCI to PCI Bridge",
0x5201 : "Network Controller",
0x5309 : "I/O Processor Address Translation Unit",
0x530D : "I/O Companion Unit Address Translation",
0x6960 : "EHCI 960 emulator",
0x7000 : "PIIX3 PCI-to-ISA Bridge (Triton II)",
0x7010 : "PIIX3 IDE Interface (Triton II)",
0x7020 : "PIIX3 USB Host Controller (Triton II)",
0x7030 : "System Controller",
0x7051 : "Intel Business Video Conferencing Card",
0x7100 : "System Controller (MTXC)",
0x7110 : "PIIX4/4E/4M ISA Bridge",
0x7111 : "PIIX4/4E/4M IDE Controller",
0x7112 : "PIIX4/4E/4M USB Interface",
0x7113 : "PIIX4/4E/4M Power Management Controller",
0x7120 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x7121 : "Graphics Controller",
0x7122 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x7123 : "Intel 82810 Graphics Controller",
0x7123 : "Intel 82810 Graphics Controller",
0x7124 : "Host-Hub Interface Bridge / DRAM Ctrlr",
0x7125 : "Intel Direct AGP 810Chipset ",
0x7126 : "Host Bridge and Memory Controller Hub",
0x7127 : "Graphics Device (FSB 133 MHz)",
0x7128 : "Host Bridge and Memory Controller Hub",
0x712A : "Host Bridge and Memory Controller Hub",
0x7180 : "Host/PCI bridge in 440LX/EX AGP chipset",
0x7181 : "AGP device in 440LX/EX AGP chipset",
0x7182 : "intel",
0x7190 : "440BX/ZX AGPset Host Bridge",
0x7191 : "440BX/ZX AGPset PCI-to-PCI bridge",
0x7192 : "440BX/ZX chipset Host-to-PCI Bridge",
0x7194 : "AC'97 Audio device",
0x7195 : "AC97 Audio Controller",
0x7196 : "AC97 Modem Controller (Winmodem)",
0x7198 : "PCI to ISA Bridge",
0x7199 : "EIDE Controller",
0x719A : "USB Universal Host Controller",
0x719B : "Power Management Controller",
0x71A0 : "Host-to-PCI Bridge",
0x71A1 : "fabricated by Intel ",
0x71A2 : "Host-to-PCI Bridge",
0x7221 : "graphics device",
0x7600 : "LPC/FWH Interface",
0x7601 : "EIDE Controller",
0x7602 : "USB Host Controller",
0x7603 : "SM Bus Controller",
0x7605 : "IEEE1394 OpenHCI Host Controller",
0x7800 : "AGP Graphics Accelerator",
0x803b : "0x81ef",
0x8083 : "Intel Wireless WiFi Link 5100 ABGN 10/100/1000 Base T",
0x8086 : "PCI-Контроллер Simple Communications",
0x8086 : "intel",
0x8086 : "VIA vynil v700b",
0x8086 : "REV_003&61AAA01&0&60 ",
0x8086 : "VIA vynil v700b",
0x8086 : "pci simple communications controller ",
0x8086 : "HDAUDIOFUNC_01&VEN_8086&DEV_1000",
0x8086 : "Intel(R) Management Engine Interface",
0x8108 : "Intel(R) Graphics Media Accelerator 500 http://downloadcenter.intel.com/Detail_Desc.aspx?lang=eng&D",
0x811A : "Atom SCH PATA",
0x8186 : "i dont know",
0x8280 : "Realtek AC97",
0x84C4 : "450KX/GX PCI Bridge (Orion)",
0x84C5 : "450KX/GX Memory Controller (Orion)",
0x84CA : "450NX PCIset Memory & I/O Controller",
0x84CB : "PCI Expander Bridge",
0x84E0 : "System Address controller",
0x84E1 : "System Data Controller",
0x84E2 : "Graphics Expander Bridge",
0x84E3 : "Memory Address Controller",
0x84E4 : "Memory Data Controller",
0x84E6 : "Wide and fast PCI eXpander Bridge",
0x84EA : "AGP Bridge (GXB function 1)",
0x85A1 : "LPC Bridge",
0x85A2 : "IDE Controller",
0x85A3 : "Serial ATA Controller",
0x85A4 : "SMBus Controller",
0x85A6 : "AC'97 Audio Controller",
0x85A7 : "AC'97 Modem Controller",
0x85A9 : "USB 1.1 UHCI Controller #1",
0x85AA : "USB 1.1 UHCI Controller #2",
0x8C3A : "Intel(R) Management Engine Interface",
0x9620 : "I2O RAID PCI to PCI Bridge",
0x9621 : "I2O 1.5 RAID Controller",
0x9622 : "I2O 1.5 RAID Controller",
0x9641 : "I2O 1.5 RAID Controller",
0x96A1 : "I2O 1.5 RAID Controller",
0x9779 : "0x2992",
0x9874 : "AUDIO CONTROLLER",
0x9876 : "intel brokdale",
0x9876 : "IntcDAudModel",
0x9877 : "1",
0x9888 : "HDAUDIOFUNC_01&VEN_8086&DEV_27d8&REV_1000",
0x9998 : " 02",
0x9999 : "Interface chip",
0x9C22 : "Intel Chipset",
0x9C3A : "Intel Management Engine Interface driver",
0xA001 : "Intel Media Accelerator 3150",
0xA002 : "Intel Grafik-Media-Accelerator 3150 (Intel GMA 3150)",
0xA011 : "Intel(R) Graphics Media Accelerator 3150",
0xA012 : "Intel Graphics Media Accelerator 3150",
0xA011 : "3&33FD14CA&0&10",
0xA012 : "Intel(R) ICH8 Family SMBus Controller",
0xB152 : "PCI to PCI Bridge",
0xB154 : "PCI to PCI Bridge",
0xB555 : "Non-Transparent PCI-to-PCI Bridge",
0xC50 : "sdf",
0xE13A : "NXMOQSN00430812D49",
0x2 : "0x27DA",
2 : "PCI/VEN_8086&DEV_2A07&SUBSYS",
0x3 : "PCIVEN_8086&DEV_3B64&SUBSYS_3B648086&REV_063&11583659&0&B0 ",
0x27c8 : "Microsoft UAA Bus HD Audio",
0x27d8 : "INTEL IDT Audio",
0x999 : "PCIVEN_8086&DEV_2930&SUBSYS_037E1014&REV_023&61AAA01&0&FB",
0x1c3a : "REV-04",
0x1E3A : "i5 2500k?",
0x3B64 : "REV_02",
0x1c3a : "REV-04 3&11583659",
0x1C3A : "Intel(R) Management Engine Interface",
8671 : "",
},
0x8087 : { 0x0028 : "MCP67 High Definition Audio",
0x07D6 : "Intel Centrino Wireless-N + WiMAX 6150",
},
0x80EE : { 0x7145 : "VirtualBox Graphics Adapter",
0xBEEF : "VirtualBox Graphics Adapter",
},
0x8866 : { 0x1685 : "MP3 player/FM radio/voice recorder 256 Mo flash",
0x1689 : "MP3 player/FM radio/voice recorder 256 Mo flash",
},
0x9004 : { 0x0078 : "AHA-2940UW/CN",
0x1078 : "RAID Coprocessor",
0x1135 : "Texas Instruments",
0x1160 : "Fibre Channel Adapter",
0x2178 : "SCSI Controller",
0x3860 : "AIC-2930U Ultra SCSI Ctrlr",
0x3B78 : "QuadChannel Fast-Wide/Ultra-Wide Diff. SCSI Ctrlr",
0x5075 : "SCSI Ctrlr",
0x5078 : "Fast/Wide SCSI Controller",
0x5175 : "SCSI Ctrlr",
0x5178 : "FAST-SCSI Ctrlr",
0x5275 : "SCSI Ctrlr",
0x5278 : "Fast SCSI Ctrlr",
0x5375 : "SCSI Ctrlr",
0x5378 : "Fast SCSI Ctrlr",
0x5475 : "SCSI Ctrlr",
0x5478 : "Fast SCSI Ctrlr",
0x5575 : "SCSI Ctrlr",
0x5578 : "Fast SCSI Ctrlr",
0x5675 : "SCSI Ctrlr",
0x5678 : "Fast SCSI Ctrlr",
0x5775 : "SCSI Ctrlr",
0x5778 : "Fast SCSI Ctrlr",
0x5800 : "PCI-to-1394 Ctrlr",
0x5900 : "ATM155 & 25 LAN Controller",
0x5905 : "ATM Adpater",
0x6038 : "Ultra SCSI Adpater (VAR)",
0x6075 : "CardBus Ultra SCSI Controller",
0x6078 : "PCI SCSI Controller",
0x6178 : "PCI SCSI Controller",
0x6278 : "SCSI Ctrlr",
0x6378 : "SCSI Ctrlr",
0x6478 : "SCSI Ctrlr",
0x6578 : "SCSI Ctrlr",
0x6678 : "SCSI Ctrlr",
0x6778 : "SCSI Ctrlr",
0x6915 : "Fast Ethernet",
0x7078 : "Fast and Wide SCSI Ctrlr",
0x7178 : "Fast/Fast-Wide SCSI Ctrlr",
0x7278 : "Multichannel Fast/Fast-Wide SCSI Ctrlr",
0x7378 : "4-chan RAID SCSI Ctrlr",
0x7478 : "SCSI Ctrlr",
0x7578 : "Multichannel Fast/Fast-Wide Diff. SCSI Ctrlr",
0x7678 : "QuadChannel Fast-Wide/Ultra-Wide Diff. SCSI Ctrlr",
0x7778 : "SCSI Ctrlr",
0x7810 : "Memory control IC",
0x7815 : "RAID + Memory Controller IC",
0x7850 : "Fast/Wide SCSI-2 Controller",
0x7855 : "Single channel SCSI Host Adapter",
0x7860 : "PCI SCSI Controller",
0x7870 : "Fast/Wide SCSI-2 Controller",
0x7871 : "SCSI",
0x7872 : "Multiple SCSI channels",
0x7873 : "Multiple SCSI channels",
0x7874 : "Differential SCSI",
0x7880 : "Fast 20 SCSI",
0x7890 : "SCSI controller",
0x7891 : "SCSI controller",
0x7892 : "SCSI controller",
0x7893 : "SCSI controller",
0x7894 : "SCSI controller",
0x7895 : "Ultra-Wide SCSI Ctrlr on AHA-2940 AHA-394x",
0x7896 : "SCSI controller",
0x7897 : "SCSI controller",
0x8078 : "Ultra Wide SCSI",
0x8178 : "Ultra/Ultra-Wide SCSI Ctrlr",
0x8278 : "AHA-3940U/3940UW/3940UWD SCSI Ctrlr",
0x8378 : "SCSI Controller",
0x8478 : "Ultra-Wide Diff. SCSI Ctrlr",
0x8578 : "Fast-Wide/Ultra-Wide Diff. SCSI Ctrlr",
0x8678 : "QuadChannel Ultra-Wide Diff. SCSI Ctrlr",
0x8778 : "Ultra-Wide SCSI Ctrlr",
0x8878 : "Ultra Wide SCSI Controller",
0x8B78 : "AIC-7880P",
0xEC78 : "QuadChannel Fast-Wide/Ultra-Wide Diff. SCSI Ctrlr",
},
0x9005 : { 0x0010 : "AHA-2940U2W/U2B",
0x0011 : "AHA-2930U2 Ultra2 SCSI Host Adapter",
0x0013 : "SCSI Controller",
0x001F : "Ultra2-Wide SCSI controller",
0x0020 : "SCSI Controller",
0x002F : "SCSI Controller",
0x0030 : "SCSI Controller",
0x003F : "SCSI Controller",
0x0050 : "AHA-3940U2x/3950U2x Ultra2 SCSI Adapter",
0x0051 : "AHA-3950U2x Ultra2 SCSI Adapter",
0x0053 : "SCSI Controller",
0x005F : "Ultra2 SCSI Controller",
0x0080 : "Ultra160/m PCI SCSI Controller",
0x0081 : "Ultra160 SCSI Controller",
0x0083 : "Ultra160 SCSI Controller",
0x008F : "Ultra160 SCSI Controller",
0x00C0 : "Ultra160 SCSI Controller",
0x00C1 : "Ultra160 SCSI Controller",
0x00C3 : "Ultra160 SCSI Controller",
0x00C5 : "RAID Subsystem HBA",
0x00CF : "Ultra160 SCSI Controller",
0x0241 : "Adaptec 1420SA Serial AHA HostRAID Controller",
0x0258 : "Adaptec AAR-2610SA SATA 6-Port Raid",
0x0285 : "PCIX133 32/64bit",
0x0286 : "SUBSYS_95801014REV_02",
0x041F : "SAS/SATA Controller",
0x043E : "SAS/SATA Controller",
0x41E : "Razor ASIC",
0x564A : "iSCSI Controller",
0x8000 : "Ultra320 SCSI Controller",
0x800F : "Ultra320 SCSI Controller",
0x8010 : "Ultra320 SCSI Controller",
0x8011 : "Ultra320 SCSI Controller",
0x8012 : "Ultra320 SCSI Controller",
0x8014 : "Ultra320 SCSI Controller",
0x8015 : "Ultra320 SCSI Controller",
0x8016 : "Ultra320 SCSI Controller",
0x8017 : "Ultra320 SCSI Controller",
0x801C : "Ultra320 SCSI Controller",
0x801D : "Ultra320 SCSI Controller",
0x801E : "Ultra320 SCSI Controller",
0x801F : "Ultra320 SCSI Controller",
0x8080 : "Ultra320 HostRAID Controller",
0x808F : "Ultra320 HostRAID Controller",
0x8090 : "HostRAID SCSI Controller",
0x8091 : "HostRAID SCSI Controller",
0x8092 : "HostRAID SCSI Controller",
0x8093 : "HostRAID SCSI Controller",
0x8094 : "HostRAID SCSI Controller",
0x8095 : "HostRAID SCSI Controller",
0x8096 : "HostRAID SCSI Controller",
0x8097 : "HostRAID SCSI Controller",
0x809C : "HostRAID SCSI Controller",
0x809D : "HostRAID SCSI Controller",
0x809E : "HostRAID SCSI Controller",
0x809F : "HostRAID SCSI Controller",
},
0x9412 : { 0x6565 : "IDE Controller?",
},
0x9710 : { 0x7705 : "MCS7705 -- USB 1.1 to Single Parallel Controller",
0x7830 : "USB 2.0 to 10/100M Fast Ethernet Controller",
0x8729 : "usb 2.0 10/100M ethernet adaptor",
0x9805 : "Netmos Parallel port PCI card",
0x9815 : "MCS9815 / M-CAB Parallel Adapter",
0x9835 : "2 serial",
0x9845 : "2 serial",
0x9865 : "PCI Porta Paralela",
0x9900 : "NetMOS Single Parallel Port Card",
0x9912 : "PCIe to Dual Serial and Single Parallel",
0x9922 : "PCIe to Dual Serial Port Controller",
},
0x9902 : { 0x0001 : "SG2010",
0x0002 : "SG2010",
0x0003 : "SG1010",
},
0xA0F1 : { 0x9876 : "0x9876",
},
0xA200 : { 0xa200 : "tv",
},
0xA259 : { 0x3038 : "USBVID_03F0&PID_0205",
},
0xA304 : { 0x3038 : "USB",
},
0xA727 : { 0x0013 : "3com 11 a/b/g wireless PCI Adapter",
},
0xAA42 : { 0x03A3 : "CharKey",
},
0xC0DE : { 0x5600 : "",
0xC0DE : "oZ0030",
},
0xD4D4 : { 0x010F : "PMC-211",
0x0601 : "PCI Mezzanine Card",
},
0xDEAF : { 0x9050 : "",
0x9051 : "",
0x9052 : "",
},
0xE159 : { 0x0001 : "Yeastar TDM400",
0x0002 : "Sedlbauer Speed PCI",
0x0600 : "PCI-to-PCI Bridge",
},
0xEACE : { 0x24C5 : "VIA Vynil v700b",
0x3100 : "OC-3/OC-12",
0x3200 : "OC-3/OC-12",
0x320E : "Fast Ethernet",
0x340E : "Fast Ethernet",
0x341E : "Fast Ethernet",
0x3500 : "OC-3/OC-12",
0x351C : "Fast Ethernet",
0x4100 : "OC-48",
0x4110 : "OC-48",
0x4200 : "OC-48",
0x420E : "Dual Gigabit Ethernet",
0x430e : "Dual Gigabit Ethernet",
},
0xECC0 : { 0x0050 : "",
0x0051 : "",
0x0060 : "",
0x0070 : "",
0x0071 : "",
0x0072 : "",
0x0080 : "4/2 channel (analog/digital) audio card",
0x0100 : "6/8 channel (analog/digital) audio card",
0x3410 : "Motorola",
},
0xEDD8 : { 0xA091 : "ARK1000PV",
0xA099 : "ARK2000PV",
0xA0A1 : "ARK2000MT",
0xA0A9 : "ARK2000MI",
0xA0B1 : "ARK2000MI+",
},
0xFA57 : { 0x0001 : "Pattern Matching Chip",
}
}
|
raisfathin/chipsec
|
source/tool/chipsec/hal/pcidb.py
|
Python
|
gpl-2.0
| 393,089
|
[
"BWA",
"CRYSTAL",
"Octopus",
"VisIt"
] |
5302928a7965b4f28dcab1f83c42dfa228176a67a962494455d9f6c0c0c547e5
|
"""
docstring needed
:copyright: Copyright 2010-2017 by the NineML Python team, see AUTHORS.
:license: BSD-3, see LICENSE for details.
"""
from nineml.exceptions import NineMLUsageError
from nineml.visitors import BaseVisitor
# Check that the sub-components stored are all of the
# right types:
class LocalNameConflictsComponentValidator(BaseVisitor):
"""
Check for conflicts between Aliases, StateVariables, Parameters, and
EventPorts, and analog input ports
We do not need to check for comflicts with output AnalogPorts, since, these
will use names.
"""
def __init__(self, component_class, **kwargs): # @UnusedVariable
BaseVisitor.__init__(self)
self.symbols = []
self.component_class = component_class
self.visit(component_class)
def check_conflicting_symbol(self, symbol):
symbol = symbol.lower()
if symbol in self.symbols:
raise NineMLUsageError(
"Found duplication of '{}' symbol in {} "
"(Note that symbols must be case-insensitively unique despite "
"being case-sensitive in general)"
.format(symbol, self.component_class))
self.symbols.append(symbol)
def action_parameter(self, parameter, **kwargs): # @UnusedVariable @IgnorePep8
self.check_conflicting_symbol(parameter.name)
def action_alias(self, alias, **kwargs): # @UnusedVariable
# Exclude aliases defined within sub scopes (as they should match the
# outer scope anyway)
if alias in self.component_class.aliases:
self.check_conflicting_symbol(alias.lhs)
def action_constant(self, constant, **kwargs): # @UnusedVariable @IgnorePep8
self.check_conflicting_symbol(constant.name)
def default_action(self, obj, nineml_cls, **kwargs):
pass
class DimensionNameConflictsComponentValidator(BaseVisitor):
def __init__(self, component_class, **kwargs): # @UnusedVariable
BaseVisitor.__init__(self)
self.dimensions = {}
self.visit(component_class)
def check_conflicting_dimension(self, dimension):
try:
if dimension != self.dimensions[dimension.name]:
err = ("Duplication of dimension name '{}' for differing "
"dimensions ('{}', '{}')"
.format(dimension.name, dimension,
self.dimensions[dimension.name]))
raise NineMLUsageError(err)
except KeyError:
self.dimensions[dimension.name] = dimension
def action_parameter(self, parameter, **kwargs): # @UnusedVariable @IgnorePep8
self.check_conflicting_dimension(parameter.dimension)
def action_constant(self, constant, **kwargs): # @UnusedVariable @IgnorePep8
self.check_conflicting_dimension(constant.units.dimension)
def default_action(self, obj, nineml_cls, **kwargs):
pass
|
INCF/lib9ML
|
nineml/abstraction/componentclass/visitors/validators/names.py
|
Python
|
bsd-3-clause
| 2,958
|
[
"VisIt"
] |
0f9d0c495722ef37ef43e05ee7aedbb5b7d7cef1acaeee91c9807abae1a46150
|
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